From owner-chemistry@ccl.net Wed Feb 19 08:50:01 2014 From: "Matthieu Montes matthieu.montes .. cnam.fr" To: CCL Subject: CCL: origin of the electrostatic potential coloring convention ? Message-Id: <-49757-140219084818-31765-ZZUaOR/37qPlcRLMojZ5sg ~ server.ccl.net> X-Original-From: Matthieu Montes Content-Type: multipart/alternative; boundary="Apple-Mail=_34B55427-4CBE-4AFD-AF0A-1B7C0F8BC93C" Date: Wed, 19 Feb 2014 14:54:00 +0100 Mime-Version: 1.0 (Mac OS X Mail 7.1 \(1827\)) Sent to CCL by: Matthieu Montes [matthieu.montes[]cnam.fr] --Apple-Mail=_34B55427-4CBE-4AFD-AF0A-1B7C0F8BC93C Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Dear CCL subscribers, I was wondering about the origin of the convention used in computational = chemistry for coloring electrostatic potentials (Blue for positive = charge, Red for negative charge). Is it originally from the = Corey/Pauling coloring of atoms (like blue for nitrogens of positively = charged amines and red for oxygens of negatively charged carboxylates ? The oldest papers regarding this subject that I could find were the = Lavery and Pullman's (1981) about electrostatic potential mapped on the = solvent accesssible surface area of DNA and the Weiner et al (1982) = about mapping electrostatic potential onto the molecular dot surface of = biomolecules.. In these papers, the convention about the choice of = colors for the potential is already there.. If you can help me address this question, I would be grateful :) With my very best regards, Matthieu -- Matthieu Montes, PhD Ma=EEtre de Conf=E9rences / Assistant Professor Laboratoire GBA D=E9partement iMATH Conservatoire National des Arts et M=E9tiers 292 Rue Saint-Martin 75003 Paris, France mailto:matthieu.montes++cnam.fr phone +33140272809 http://gba.cnam.fr/ --Apple-Mail=_34B55427-4CBE-4AFD-AF0A-1B7C0F8BC93C Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 Dear = CCL subscribers,

I was wondering about the origin of = the convention used in computational chemistry for coloring = electrostatic potentials (Blue for positive charge, Red for negative = charge). Is it originally from the Corey/Pauling coloring of atoms (like = blue for nitrogens of positively charged amines and red for oxygens of = negatively charged carboxylates ?

The oldest = papers regarding this subject that I could find were the Lavery and = Pullman's (1981) about electrostatic potential mapped on the solvent = accesssible surface area of DNA and the Weiner et al (1982) about = mapping electrostatic potential onto the molecular dot surface of = biomolecules.. In these papers, the convention about the choice of = colors for the potential is already there..

If = you can help me address this question, I would be grateful = :)

With my very best = regards,

Matthieu

Matthieu Montes, = PhD
Ma=EEtre de Conf=E9rences / Assistant = Professor
Laboratoire GBA
D=E9partement = iMATH
Conservatoire National des Arts et M=E9tiers
292= Rue Saint-Martin
75003 Paris, France
mailto:matthieu.montes++cnam.fr=
phone +33140272809
http://gba.cnam.fr/


= --Apple-Mail=_34B55427-4CBE-4AFD-AF0A-1B7C0F8BC93C-- From owner-chemistry@ccl.net Wed Feb 19 09:25:00 2014 From: "CARLOS SIMMERLING carlos.simmerling|stonybrook.edu" To: CCL Subject: CCL: ACS COMP Division student and junior faculty awards for Fall 2014 meet Message-Id: <-49758-140219085333-1235-9+rz332vcV2axh6m+/ftOw#,#server.ccl.net> X-Original-From: "CARLOS SIMMERLING" Date: Wed, 19 Feb 2014 08:53:31 -0500 Sent to CCL by: "CARLOS SIMMERLING" [carlos.simmerling---stonybrook.edu] Dear colleagues, The ACS Division of Computers in Chemistry (COMP) is offering awards for outstanding graduate students and junior faculty members to attend the Fall 2014 ACS National Meeting. Support for these awards is provided by COMP, The Chemical Computing Group, and OpenEye Scientific Software. The deadline for applying is March 11, 2014. Graduate student award: http://web2011.acscomp.org/awards/chemical-computing- group-excellence-award Junior faculty award: http://web2011.acscomp.org/awards/the-comp-acs- outstanding-junior-faculty-award We especially encourage those from traditionally underrepresented groups to apply for these awards. Please share this announcement with any parties that may be interested. Best regards, The ACS Division of Computers in Chemistry (COMP) From owner-chemistry@ccl.net Wed Feb 19 11:03:00 2014 From: "Vivek Sharma vivek.viv.sharma- -gmail.com" To: CCL Subject: CCL: origin of the electrostatic potential coloring convention ? Message-Id: <-49759-140219105923-7578-C/PmJeBNd47wxWA7pcqBpg]![server.ccl.net> X-Original-From: Vivek Sharma Content-Type: multipart/alternative; boundary=047d7b41904b5550a504f2c4782f Date: Wed, 19 Feb 2014 17:59:13 +0200 MIME-Version: 1.0 Sent to CCL by: Vivek Sharma [vivek.viv.sharma^_^gmail.com] --047d7b41904b5550a504f2c4782f Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello, i think it may have to do with pH coloring scheme, blue for basic and red for acidic. Best regards, Vivek On Feb 19, 2014 5:26 PM, "Matthieu Montes matthieu.montes .. cnam.fr" < owner-chemistry#%#ccl.net> wrote: > Dear CCL subscribers, > > I was wondering about the origin of the convention used in computational > chemistry for coloring electrostatic potentials (Blue for positive charge= , > Red for negative charge). Is it originally from the Corey/Pauling colorin= g > of atoms (like blue for nitrogens of positively charged amines and red fo= r > oxygens of negatively charged carboxylates ? > > The oldest papers regarding this subject that I could find were the Laver= y > and Pullman's (1981) about electrostatic potential mapped on the solvent > accesssible surface area of DNA and the Weiner et al (1982) about mapping > electrostatic potential onto the molecular dot surface of biomolecules.. = In > these papers, the convention about the choice of colors for the potential > is already there.. > > If you can help me address this question, I would be grateful :) > > With my very best regards, > > Matthieu > > -- > > Matthieu Montes, PhD > Ma=EEtre de Conf=E9rences / Assistant Professor > Laboratoire GBA > D=E9partement iMATH > Conservatoire National des Arts et M=E9tiers > 292 Rue Saint-Martin > 75003 Paris, France > mailto:matthieu.montes]|[cnam.fr > phone +33140272809 > http://gba.cnam.fr/ > > > --047d7b41904b5550a504f2c4782f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hello, i think it may have to do with pH coloring scheme, blue for basic= and red for acidic.

Best regards,

Vivek

On Feb 19, 2014 5:26 PM, "Matthieu Montes m= atthieu.montes .. cnam.fr" <owner-chemistry#%#ccl.net> wrote:<= br type=3D"attribution">
Dear CCL= subscribers,

I was wondering about the origin of the co= nvention used in computational chemistry for coloring electrostatic potenti= als (Blue for positive charge, Red for negative charge). Is it originally f= rom the Corey/Pauling coloring of atoms (like blue for nitrogens of positiv= ely charged amines and red for oxygens of negatively charged carboxylates ?=

The oldest papers regarding this subject that I could f= ind were the Lavery and Pullman's (1981) about electrostatic potential = mapped on the solvent accesssible surface area of DNA and the Weiner et al = (1982) about mapping electrostatic potential onto the molecular dot surface= of biomolecules.. In these papers, the convention about the choice of colo= rs for the potential is already there..

If you can help me address this question, I would be gr= ateful :)

With my very best regards,
Matthieu

--

Matthieu Montes, PhD
Ma=EEtre de Conf= =E9rences / Assistant Professor
Laboratoire GBA
D=E9par= tement iMATH
Conservatoire National des Arts et M=E9tiers
292 Rue Saint-Martin
75003 Paris, France
http://gba.cnam.fr/

--047d7b41904b5550a504f2c4782f-- From owner-chemistry@ccl.net Wed Feb 19 12:32:00 2014 From: "zborowsk zborowsk+*+chemia.uj.edu.pl" To: CCL Subject: CCL: ICQC shame Message-Id: <-49760-140219100142-10560-gcewh3qkAKEVexaDesrbMg!A!server.ccl.net> X-Original-From: zborowsk Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 19 Feb 2014 16:01:32 +0100 MIME-Version: 1.0 Sent to CCL by: zborowsk [zborowsk(0)chemia.uj.edu.pl] Hello! Just to clarify my previous message. Of course, I am not a native english speaker. If there is something wrong about that I propose that native english speakers should try to write something in correct Polish language. By the way, the most discriminative thing in the science is that some people can use their mother language while others must lost a lot of time learning English. For sure, this kind of discrimination should be taken into account! But this time I knew what word should I use, according to the modern nomenclature. Simply, the gender ideology try to be present everywhere, so it is impossible not to know what gender means. Yes, I used “sex” because I wanted to be a bit provocative and check in a simple way for how many persons the most important thing is “nomenclature”, not the matter of the problem. And the problem is that scientists should not be evaluated using non-scientific criteria. Sex is probably the last thing that should be taken into accout. It is very strange for me that where I see 24 very good lecturers anybody see 24 males. If there will be 24 women I still see 24 good lectureres, nothing else. I think thats all. As some other members of the CCL community I think I have more urgent things than gender. Ok, one more thing. The comment: “it is also intetesting that a man who does not know the difference between gender and sex can want to talk about theoretical chemistry!!!” Is probably the most st....range I have ever read. For sure on CCL. I know what is gender, but I COMPLETELY SURE THAT THIS KIND OF KNOWLEDGE IS NOT IMPORTANT IF I WANT TO TALK ABOUT PHYSICS. Have you ever read in the scientific manuscript phrases like these?? “Calculations have been performed in the Gender regime. The quality of the results have been improved by using the aug-Gender-TZ basis set. The numbers or male and female electrons have been carefully balanced, etc...” Maybe, in near future, the Author of the mentioned comment use them, who knows. Best regards Kżyś From owner-chemistry@ccl.net Wed Feb 19 13:06:00 2014 From: "Duke, Robert E Jr rduke!=!email.unc.edu" To: CCL Subject: CCL: origin of the electrostatic potential coloring convention ? Message-Id: <-49761-140219122803-6825-GsyM0a05gkrt1AbOzjm9Zw/./server.ccl.net> X-Original-From: "Duke, Robert E Jr" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_129A87CAD90E384C93AC78D2ACBAB8034533AE5BITSMSXMBS4Madun_" Date: Wed, 19 Feb 2014 17:27:50 +0000 MIME-Version: 1.0 Sent to CCL by: "Duke, Robert E Jr" [rduke[*]email.unc.edu] --_000_129A87CAD90E384C93AC78D2ACBAB8034533AE5BITSMSXMBS4Madun_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Sounds like litmus test colors to me, guys (you know, most basic bench test= for acidic/basic solutions, before invention of pH electrodes). ________________________________ > From: owner-chemistry+rduke=3D=3Demail.unc.edu|a|ccl.net [owner-chemistry+rdu= ke=3D=3Demail.unc.edu|a|ccl.net] on behalf of Vivek Sharma vivek.viv.sharma- = -gmail.com [owner-chemistry|a|ccl.net] Sent: Wednesday, February 19, 2014 7:59 AM To: Duke, Robert E Jr Subject: CCL: origin of the electrostatic potential coloring convention ? Hello, i think it may have to do with pH coloring scheme, blue for basic an= d red for acidic. Best regards, Vivek On Feb 19, 2014 5:26 PM, "Matthieu Montes matthieu.montes .. cnam.fr" > wr= ote: Dear CCL subscribers, I was wondering about the origin of the convention used in computational ch= emistry for coloring electrostatic potentials (Blue for positive charge, Re= d for negative charge). Is it originally from the Corey/Pauling coloring of= atoms (like blue for nitrogens of positively charged amines and red for ox= ygens of negatively charged carboxylates ? The oldest papers regarding this subject that I could find were the Lavery = and Pullman's (1981) about electrostatic potential mapped on the solvent ac= cesssible surface area of DNA and the Weiner et al (1982) about mapping ele= ctrostatic potential onto the molecular dot surface of biomolecules.. In th= ese papers, the convention about the choice of colors for the potential is = already there.. If you can help me address this question, I would be grateful :) With my very best regards, Matthieu -- Matthieu Montes, PhD Ma=EEtre de Conf=E9rences / Assistant Professor Laboratoire GBA D=E9partement iMATH Conservatoire National des Arts et M=E9tiers 292 Rue Saint-Martin 75003 Paris, France mailto:matthieu.montes]|[cnam.fr phone +33140272809 http://gba.cnam.fr/ --_000_129A87CAD90E384C93AC78D2ACBAB8034533AE5BITSMSXMBS4Madun_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Sounds like litmus test colors to me, guys (you know, most basic ben= ch test for acidic/basic solutions, before invention of pH electrodes).
From: owner-chemistry+rduke=3D=3Demai= l.unc.edu|a|ccl.net [owner-chemistry+rduke=3D=3Demail.unc.edu|a|ccl.net] on= behalf of Vivek Sharma vivek.viv.sharma- -gmail.com [owner-chemistry|a|ccl.n= et]
Sent: Wednesday, February 19, 2014 7:59 AM
To: Duke, Robert E Jr
Subject: CCL: origin of the electrostatic potential coloring convent= ion ?

Hello, i think it may have to do with pH coloring scheme, blue for basic= and red for acidic.

Best regards,

Vivek

On Feb 19, 2014 5:26 PM, "Matthieu Montes m= atthieu.montes .. cnam.fr" <owner-chemistry]![c= cl.net> wrote:
Dear CCL subscribers,

I was wondering about the origin of the convention used in computation= al chemistry for coloring electrostatic potentials (Blue for positive charg= e, Red for negative charge). Is it originally from the Corey/Pauling colori= ng of atoms (like blue for nitrogens of positively charged amines and red for oxygens of negatively charged car= boxylates ?

The oldest papers regarding this subject that I could find were the La= very and Pullman's (1981) about electrostatic potential mapped on the solve= nt accesssible surface area of DNA and the Weiner et al (1982) about mappin= g electrostatic potential onto the molecular dot surface of biomolecules.. In these papers, the convention ab= out the choice of colors for the potential is already there..

If you can help me address this question, I would be grateful :)

With my very best regards,

Matthieu

--

Matthieu Montes, PhD
Ma=EEtre de Conf=E9rences / Assistant Professor
Laboratoire GBA
D=E9partement iMATH
Conservatoire National des Arts et M=E9tiers
292 Rue Saint-Martin
75003 Paris, France
http://gba.cnam.fr/

--_000_129A87CAD90E384C93AC78D2ACBAB8034533AE5BITSMSXMBS4Madun_-- From owner-chemistry@ccl.net Wed Feb 19 13:41:00 2014 From: "Mike Towler mdt26-.-cam.ac.uk" To: CCL Subject: CCL:G: GAUSSIAN/GAMESS/MOLPRO/CRYSTAL: different energies - f function basis Message-Id: <-49762-140219123010-7337-8UBvoV/Hs7aRqAksO07kdA],[server.ccl.net> X-Original-From: "Mike Towler" Date: Wed, 19 Feb 2014 12:30:08 -0500 Sent to CCL by: "Mike Towler" [mdt26*cam.ac.uk] Hello, I'm one of the authors of the CASINO program - a widely-used quantum Monte Carlo code: http://vallico.net/casinoqmc/ . The way QMC works, CASINO reads a 'trial wave function' generated by an external code using e.g. a Hartree-Fock or a DFT calculation, and then it proceeds to 'improve the answer' (details irrelevant). I'm therefore responsible for maintaining interfaces between CASINO and other people's software - a list of the fifteen codes we supposedly support is here: http://vallico.net/casinoqmc/interfaces For the purposes of my present question, this list includes GAUSSIAN, GAMESS, CRYSTAL, and MOLPRO. I've recently started a formal check of the way these interfaces handle higher angular momentum Gaussian functions (by which I mean f and g along with d for completeness). The complexity of the expressions and the different conventions in use mean that this sort of thing is very easy to screw up. Basic checks are simple enough, since (1) CASINO does a numerical check of its own analytic derivatives (it needs the value of the orbitals, the gradient, and the Laplacian at random points in configuration space), and (2) CASINO is capable of running in pure Hartree-Fock mode, and thus through Monte Carlo numerical integration it should be able to give the same Hartree-Fock energy (within statistical error bars) as the code that generated the trial wave function. To check the different angular momenta individually, I've created a set of three input files for the methane molecule, with only d functions in the basis, only f functions, and only g functions (let's call them 'd-ane', 'f-ane', and 'g-ane'). However, before we even get to CASINO, and looking first at f-ane, we've found that the four codes above give very different answers for the Hartree-Fock energy. In fact GAUSSIAN and CRYSTAL give -11.3966 au, but both GAMESS and MOLPRO give -11.2286 au. (For the record, CASINO agrees with GAUSSIAN and CRYSTAL for the HF energy when fed with their trial wave functions. It's not been possible to check with GAMESS and MOLPRO as their current interfaces to CASINO don't yet support f functions.. though they will shortly.) Now I don't have the experience or any access to any of these codes apart > from CRYSTAL (I got some kind colleagues to run the calculations for me), so it's difficult for me to see why this difference exists, and my colleagues aren't sure either. There was some suggestion that it might be to do with the spherical/Cartesian basis set conversion? So I was wondering, are there any GAMESS, GAUSSIAN, or MOLPRO gurus out there who can shed any light on this problem? It seems strange that such well-known codes would give such different answers for such a simple system. The input files for the four codes are here: http://www.tcm.phy.cam.ac.uk/~mdt26/g/crystal.txt http://www.tcm.phy.cam.ac.uk/~mdt26/g/gamess.txt http://www.tcm.phy.cam.ac.uk/~mdt26/g/gaussian.txt http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro1.txt http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro2.txt Any assistance will be gratefully appreciated. Thanks, Mike Towler From owner-chemistry@ccl.net Wed Feb 19 14:16:01 2014 From: "Frank Marchese ftmarchese||yahoo.com" To: CCL Subject: CCL: origin of the electrostatic potential coloring convention ? Message-Id: <-49763-140219133626-16078-Gito25TBoob+RABdUEufRQ_+_server.ccl.net> X-Original-From: Frank Marchese Content-Type: multipart/alternative; boundary="756480036-1107848427-1392834976=:82031" Date: Wed, 19 Feb 2014 10:36:16 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Frank Marchese [ftmarchese__yahoo.com] --756480036-1107848427-1392834976=:82031 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Feldman and coworkers use various schemes=A0 to color protein surfaces. For= electrostatics:=0A=0A"To appreciate the forces associated with the binding= of two molecular surfaces, the surface of trypsin is coded in terms of=0Ac= olor to identify regions of hydrophobicity, hydrophilicity, and charge. Hyd= rophobic atoms are indicated by black, hydrophilic uncharged atoms by white= , positively charged atoms by blue, and negatively charged atoms by red. In= termediate shades of black, blue, and red indicate intermediate degrees of = hydrophobicity, electropositivity, or electronegativity, respectively."=0A= =0AThey also discuss issues of pH relative to the coloring scheme.=0A=0A=0A= Feldmann, Richard J., et al. "Interactive computer surface graphics approac= h to study of the active site of bovine trypsin." Proceedings of the Nation= al Academy of Sciences 75.11 (1978): 5409-5412.=0A=0A=A0=0A=0ADr. Francis T= . Marchese=0A=0AProfessor=0ADept. of Computer Science=0APace University=0A1= 63 William Street, 2nd Floor=0ANew York, NY 10038=0Ahttp://csis.pace.edu/~m= archese=0Aemail: fmarchese^^pace.edu=0Aphone: 212 346-1803=0A=0ACo-director,= Pace Digital Gallery=0Ahttp://www.pace.edu/DigitalGallery=0A=0A=0A________= ________________________=0A From: Matthieu Montes matthieu.montes .. cnam.f= r =0ATo: "Marchese, Francis Thomas " =0ASent: Wednesday, February 19, 2014 8:54 AM=0ASubject: CC= L: origin of the electrostatic potential coloring convention ?=0A =0A=0A=0A= Dear CCL subscribers,=0A=0AI was wondering about the origin of the conventi= on used in computational chemistry for coloring electrostatic potentials (B= lue for positive charge, Red for negative charge). Is it originally from th= e Corey/Pauling coloring of atoms (like blue for nitrogens of positively ch= arged amines and red for oxygens of negatively charged carboxylates ?=0A=0A= The oldest papers regarding this subject that I could find were the Lavery = and Pullman's (1981) about electrostatic potential mapped on the solvent ac= cesssible surface area of DNA and the Weiner et al (1982) about mapping ele= ctrostatic potential onto the molecular dot surface of biomolecules.. In th= ese papers, the convention about the choice of colors for the potential is = already there..=0A=0AIf you can help me address this question, I would be g= rateful :)=0A=0AWith my very best regards,=0A=0AMatthieu=0A=0A=0A--=0A=0AMa= tthieu Montes, PhD=0AMa=EEtre de Conf=E9rences / Assistant Professor=0ALabo= ratoire GBA=0AD=E9partement iMATH=0AConservatoire National des Arts et M=E9= tiers=0A292 Rue Saint-Martin=0A75003 Paris, France=0Amailto:matthieu.montes= ]|[cnam.fr=0Aphone +33140272809http://gba.cnam.fr/ --756480036-1107848427-1392834976=:82031 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Feldman and coworkers use various schemes  to color= protein surfaces. For electrostatics:

"To appreciate the forces associated with the bi= nding of two molecular surfaces, the surface of trypsin is coded in terms o= f
color to identify regions of hydrophobicity, hydrophilicity, and charg= e. Hydrophobic atoms are indicated by black, hydrophilic uncharged atoms by= white, positively charged atoms by blue, and negatively charged atoms by r= ed. Intermediate shades of black, blue, and red indicate intermediate degre= es of hydrophobicity, electropositivity, or electronegativity, respectively."

<= div style=3D"color: rgb(0, 0, 0); font-size: 13.3333px; font-family: Helvet= icaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background= -color: transparent; font-style: normal;">They also discuss issues of pH re= lative to the coloring scheme.

Feldmann, Richard J., et al. "Int= eractive computer surface graphics approach to study of the active site of = bovine trypsin." Proceedings of the National Academy of Sciences 75.11 (197= 8): 5409-5412.
 

Dr. Francis T. Marchese

Professor
Dept. of Computer Science
Pace University=
163 William Street, 2nd Floor
New York, NY 10038
http://csis.pace.edu/~mar= chese
email: fmarchese^^pace.edu
phone: 212 346-1803

Co-director, Pa= ce Digital Gallery
http://www.pace.edu/DigitalGallery

=
From: Matthie= u Montes matthieu.montes .. cnam.fr <owner-chemistry^^ccl.net>
= To: "Marchese, Francis Thomas -id#= 3rm-" <fmarchese^^pace.edu>
Sent: Wednesday, February 19, 2014 8:54 AM
Subject: CCL: origin of the electrostati= c potential coloring convention ?

Dear CCL subscribers,

<= /div>
I was wondering about the origin of the convention used in comput= ational chemistry for coloring electrostatic potentials (Blue for positive = charge, Red for negative charge). Is it originally from the Corey/Pauling c= oloring of atoms (like blue for nitrogens of positively charged amines and = red for oxygens of negatively charged carboxylates ?

The oldest papers regarding this subject that I could find were the Lave= ry and Pullman's (1981) about electrostatic potential mapped on the solvent accesssible surface area of DNA and the Weiner et al (1982) about mapping = electrostatic potential onto the molecular dot surface of biomolecules.. In= these papers, the convention about the choice of colors for the potential = is already there..

If you can help me address this= question, I would be grateful :)

With my very bes= t regards,

Matthieu

=0A
--

Matthieu Montes, = PhD
Ma=EEtre de Conf=E9rences / Assistant Professor
Lab= oratoire GBA
D=E9partement iMATH
Conservatoire National= des Arts et M=E9tiers
292 Rue Saint-Martin
75003 Paris= , France
phone +33140272809
http://gba.cnam.fr/

=0A
=0A


=
--756480036-1107848427-1392834976=:82031-- From owner-chemistry@ccl.net Wed Feb 19 15:27:00 2014 From: "Alan Shusterman alan]_[reed.edu" To: CCL Subject: CCL: origin of the electrostatic potential coloring convention ? Message-Id: <-49764-140219142044-14165-aJyUN+KK0ZeNKPX9Dxef5g|,|server.ccl.net> X-Original-From: Alan Shusterman Content-Type: multipart/alternative; boundary="------------040001020106070902040806" Date: Wed, 19 Feb 2014 11:20:41 -0800 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan*o*reed.edu] This is a multi-part message in MIME format. --------------040001020106070902040806 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit A conversation that I had with Warren Hehre in 1989: Alan: Why are you using red for negative potentials, blue for positive? Warren: Red is the low-energy end of the visual spectrum. Blue is the high-energy end. Also, red things are "hot" and you want to see which molecules are hotter nucleophiles by looking for red zones. This rationale, red (energy) < blue (energy), applies to all of the maps displayed in Spartan: potentials, orbital amplitudes, electron density, ... Alan On 2/19/2014 7:59 AM, Vivek Sharma vivek.viv.sharma- -gmail.com wrote: > > Hello, i think it may have to do with pH coloring scheme, blue for > basic and red for acidic. > > Best regards, > > Vivek > > On Feb 19, 2014 5:26 PM, "Matthieu Montes matthieu.montes .. cnam.fr > " > wrote: > > Dear CCL subscribers, > > I was wondering about the origin of the convention used in > computational chemistry for coloring electrostatic potentials > (Blue for positive charge, Red for negative charge). Is it > originally from the Corey/Pauling coloring of atoms (like blue for > nitrogens of positively charged amines and red for oxygens of > negatively charged carboxylates ? > > The oldest papers regarding this subject that I could find were > the Lavery and Pullman's (1981) about electrostatic potential > mapped on the solvent accesssible surface area of DNA and the > Weiner et al (1982) about mapping electrostatic potential onto the > molecular dot surface of biomolecules.. In these papers, the > convention about the choice of colors for the potential is already > there.. > > If you can help me address this question, I would be grateful :) > > With my very best regards, > > Matthieu > > -- > > Matthieu Montes, PhD > Matre de Confrences / Assistant Professor > Laboratoire GBA > Dpartement iMATH > Conservatoire National des Arts et Mtiers > 292 Rue Saint-Martin > 75003 Paris, France > mailto:matthieu.montes]|[cnam.fr > phone +33140272809 > http://gba.cnam.fr/ > > -- Alan Shusterman Chemistry Department Reed College 3203 SE Woodstock Blvd Portland, OR 97202-8199 503-517-7699 http://blogs.reed.edu/alan/ "Nature doesn't make long speeches." Lao Tzu 23 --------------040001020106070902040806 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit A conversation that I had with Warren Hehre in 1989:
Alan: Why are you using red for negative potentials, blue for positive?
Warren: Red is the low-energy end of the visual spectrum. Blue is the high-energy end. Also, red things are "hot" and you want to see which molecules are hotter nucleophiles by looking for red zones.

This rationale, red (energy) < blue (energy), applies to all of the maps displayed in Spartan: potentials, orbital amplitudes, electron density, ...

Alan

On 2/19/2014 7:59 AM, Vivek Sharma vivek.viv.sharma- -gmail.com wrote:

Hello, i think it may have to do with pH coloring scheme, blue for basic and red for acidic.

Best regards,

Vivek

On Feb 19, 2014 5:26 PM, "Matthieu Montes matthieu.montes .. cnam.fr" <owner-chemistry]![ccl.net> wrote:
Dear CCL subscribers,

I was wondering about the origin of the convention used in computational chemistry for coloring electrostatic potentials (Blue for positive charge, Red for negative charge). Is it originally from the Corey/Pauling coloring of atoms (like blue for nitrogens of positively charged amines and red for oxygens of negatively charged carboxylates ?

The oldest papers regarding this subject that I could find were the Lavery and Pullman's (1981) about electrostatic potential mapped on the solvent accesssible surface area of DNA and the Weiner et al (1982) about mapping electrostatic potential onto the molecular dot surface of biomolecules.. In these papers, the convention about the choice of colors for the potential is already there..

If you can help me address this question, I would be grateful :)

With my very best regards,

Matthieu

--

Matthieu Montes, PhD
Maître de Conférences / Assistant Professor
Laboratoire GBA
Département iMATH
Conservatoire National des Arts et Métiers
292 Rue Saint-Martin
75003 Paris, France
http://gba.cnam.fr/

 


-- 
Alan Shusterman
Chemistry Department
Reed College
3203 SE Woodstock Blvd
Portland, OR 97202-8199
503-517-7699
http://blogs.reed.edu/alan/
"Nature doesn't make long speeches." Lao Tzu 23
--------------040001020106070902040806-- From owner-chemistry@ccl.net Wed Feb 19 16:02:01 2014 From: "Michel Petitjean petitjean.chiral_._gmail.com" To: CCL Subject: CCL: Exercise for students (was: ICQC shame) Message-Id: <-49765-140219142101-14506-E6crDHqgNHE/cWGbsuUmzQ() server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 19 Feb 2014 20:20:54 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral%x%gmail.com] Hello! 24 good lectures: no doubt that it could be true: there are much more than 24 good theoretical chemists over the world. Here follows my exercise for students. Let p be the proportion of women in the theoretical chemists poupulation, to be estimated as you like. Generate a sample of size n=24 from the parent population Prob(woman)=p, Prob(man)=1-p. What is the probability to get 0 women in that sample? Are the speakers taken at random? Nothing of interest to be concluded? Women did not work hard? Repeat this calculus 15 times, over the 15 ICQC Conferences, with similar n and p values. Observed numbers of women: 0,0,0,0,...,0 (15 times). What is the overall probability to observe these 15 zeroes? Still nothing of interest to be concluded? Nothing to see apart that all lectures were good? Yes I agree: I am not in favor of selecting on the basis of gender or sex. I am in favor to select on the basis of science. It is exactly what was not done. Fortunately the Chinese Organizers of ICQC 2015 seem to realize that. I invite the reader interested by the topic to read the biography of Marie Curie, born Maria Sklodowska in Warsaw (thanks to Poland to have produced such a woman). She would surely have much to say there (unfortunately that is not possible). Yes it is time to deal with science, not with gender. Until now that was not the the case. Best regards, Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral#%#gmail.com (preferred), michel.petitjean#%#univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html 2014-02-19 16:01 GMT+01:00 zborowsk zborowsk+*+chemia.uj.edu.pl : > > Sent to CCL by: zborowsk [zborowsk(0)chemia.uj.edu.pl] > Hello! > Just to clarify my previous message. Of course, I am not a native english speaker. If there is something wrong about that I propose that native english speakers should try to write something in correct Polish language. > By the way, the most discriminative thing in the science is that some people can use their mother language while others must lost a lot of time learning > English. For sure, this kind of discrimination should be taken into account! > But this time I knew what word should I use, according to the modern nomenclature. Simply, the gender ideology try to be present everywhere, so it is impossible not to know what gender means. > Yes, I used “sex” because I wanted to be a bit provocative and check in a simple way for how many persons the most important thing is “nomenclature”, not the matter of the problem. > And the problem is that scientists should not be evaluated using non-scientific criteria. Sex is probably the last thing that should be taken into accout. It is very strange for me that where I see 24 very good lecturers anybody see 24 males. If there will be 24 women I still see 24 good lectureres, nothing else. > > I think thats all. As some other members of the CCL community I think I have more urgent things than gender. > > Ok, one more thing. > The comment: “it is also intetesting that a man who does not know the difference between gender and sex can want to talk about theoretical chemistry!!!” > Is probably the most st....range I have ever read. For sure on CCL. I know what is gender, but I COMPLETELY SURE THAT THIS KIND OF KNOWLEDGE IS NOT > IMPORTANT IF I WANT TO TALK ABOUT PHYSICS. Have you ever read in the scientific manuscript phrases like these?? > “Calculations have been performed in the Gender regime. The quality of the results have been improved by using the aug-Gender-TZ basis set. The numbers or male and female electrons have been carefully balanced, etc...” > Maybe, in near future, the Author of the mentioned comment use them, who knows. > > Best regards > Kżyś > From owner-chemistry@ccl.net Wed Feb 19 16:37:00 2014 From: "Susi Lehtola susi.lehtola[#]alumni.helsinki.fi" To: CCL Subject: CCL:G: GAUSSIAN/GAMESS/MOLPRO/CRYSTAL: different energies - f function basis Message-Id: <-49766-140219145749-15178-DTdKt0mul30I2lpRF2Bdmg+/-server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Wed, 19 Feb 2014 21:57:38 +0200 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola.|,|.alumni.helsinki.fi] On Wed, 19 Feb 2014 12:30:08 -0500 "Mike Towler mdt26-.-cam.ac.uk" wrote: > To check the different angular momenta individually, I've created a set of > three input files for the methane molecule, with only d functions in the > basis, only f functions, and only g functions (let's call them 'd-ane', > 'f-ane', and 'g-ane'). > > However, before we even get to CASINO, and looking first at f-ane, we've > found that the four codes above give very different answers for the > Hartree-Fock energy. In fact GAUSSIAN and CRYSTAL give -11.3966 au, but > both GAMESS and MOLPRO give -11.2286 au. > > Now I don't have the experience or any access to any of these codes apart > > from CRYSTAL (I got some kind colleagues to run the calculations for me), > so it's difficult for me to see why this difference exists, and my > colleagues aren't sure either. There was some suggestion that it might be > to do with the spherical/Cartesian basis set conversion? So I was > wondering, are there any GAMESS, GAUSSIAN, or MOLPRO gurus out there who > can shed any light on this problem? It seems strange that such well-known > codes would give such different answers for such a simple system. There's no problem here. I checked the GAUSSIAN result, and indeed I get the same energy -11.3966 au. I ran the test also with ERKALE, which gives -11.2286 au. So there is something odd here. However, if you put in Guess=Core into the Gaussian run, you'll converge to -11.2286 au. The reason why you get two different energies is that the runs converge to different solutions. If you run an optimizing stability analysis (Stable=(Opt,RRHF) in Gaussian for spin-restricted analysis), you'll see that the -11.2286 au. solution is a saddle point, and that the local minimum the program will converge into has energy -11.3966 au. -- --------------------------------------------------------------- Mr. Susi Lehtola, PhD Research Associate susi.lehtola|,|alumni.helsinki.fi Department of Applied Physics http://www.helsinki.fi/~jzlehtol Aalto University Finland --------------------------------------------------------------- Susi Lehtola, FT Tutkijatohtori susi.lehtola|,|alumni.helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Aalto-yliopisto --------------------------------------------------------------- From owner-chemistry@ccl.net Wed Feb 19 17:12:00 2014 From: "Mikael Johansson mikael.johansson~~iki.fi" To: CCL Subject: CCL:G: GAUSSIAN/GAMESS/MOLPRO/CRYSTAL: different energies - f function basis Message-Id: <-49767-140219154142-8762-Ji4GHf3KaZ8GR3QaYqdIXg%a%server.ccl.net> X-Original-From: Mikael Johansson Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Wed, 19 Feb 2014 22:41:29 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson/./iki.fi] Hello Mike, On Wed, 19 Feb 2014, Mike Towler mdt26-.-cam.ac.uk wrote: > I've recently started a formal check of the way these interfaces handle > higher angular momentum Gaussian functions (by which I mean f and g > along with d for completeness). > To check the different angular momenta individually, I've created a set > of three input files for the methane molecule, with only d functions in > the basis, only f functions, and only g functions > looking first at f-ane, we've found that the four codes above give very > different answers for the Hartree-Fock energy. In fact GAUSSIAN and > CRYSTAL give -11.3966 au, but both GAMESS and MOLPRO give -11.2286 au. > There was some suggestion that it might be to do with the > spherical/Cartesian basis set conversion? No, your problem doesn't lie with spherical/Cartesian functions (all the codes you've tried have used spherical functions for your calcs; with Cartesian functions, the energy would be around -19.4216 Hartree). Instead, the problem is that a symmetry-broken solution (of lower symmetry than the Td sym of your molecule) lies lower in energy. Apparently GAMESS and MOLPRO preserve symmetry for the wave function (at least Abelian symmetry), while GAUSSIAN and CRYSTAL break it with the reward of a lower total energy. I suggest you start out with systems that have no symmetry and an even simpler basis set with fewer functions to get around this problem. Still, you should be careful. With "silly" basis sets the probability of the SCF converging to a saddle point or wrong minimum increases. Good luck, Mikael J. http://www.iki.fi/~mpjohans/ From owner-chemistry@ccl.net Wed Feb 19 17:46:00 2014 From: "Joy Ku joyku{:}stanford.edu" To: CCL Subject: CCL: WORKSHOP: Molecular Dynamics Simulation & Analysis, Stanford Univ. Message-Id: <-49768-140219161208-27609-CyCsZSqo7KvyT5nC12+6BQ=server.ccl.net> X-Original-From: "Joy Ku" Date: Wed, 19 Feb 2014 16:12:01 -0500 Sent to CCL by: "Joy Ku" [joyku()stanford.edu] Molecular Dynamics Simulation and Analysis Workshop March 31 April 1, 2014 This two-day workshop at Stanford University is intended for those interested in: - Accelerating MD simulations on GPUs - Having a framework for quickly developing and implementing new MD algorithms - Discovering new tools to enhance their MD simulations and the analysis of them You will gain hands-on experience with tools such as PDBFixer, which easily prepares PDB files for MD simulations; OpenMM for rapid MD simulations on GPUs and CPUs; MSMBuilder for analyzing MD trajectories using Markov State Models; and MDTraj, which provides many trajectory analysis and manipulation tools. For more details and registration information, visit http://simbios.stanford.edu/mdworkshop.htm. From owner-chemistry@ccl.net Wed Feb 19 18:21:00 2014 From: "Susi Lehtola susi.lehtola]=[alumni.helsinki.fi" To: CCL Subject: CCL: Exercise for students (was: ICQC shame) Message-Id: <-49769-140219164454-14339-ADwn8SxaKp8k1NU3F9W5Pw:server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 19 Feb 2014 23:44:41 +0200 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola^_^alumni.helsinki.fi] On Wed, 19 Feb 2014 20:20:54 +0100 "Michel Petitjean petitjean.chiral_._gmail.com" wrote: > What is the probability to get 0 women in that sample? > Are the speakers taken at random? > Nothing of interest to be concluded? > Women did not work hard? > Repeat this calculus 15 times, over the 15 ICQC Conferences, with > similar n and p values. > Observed numbers of women: 0,0,0,0,...,0 (15 times). > What is the overall probability to observe these 15 zeroes? > Still nothing of interest to be concluded? > Nothing to see apart that all lectures were good? Please, lets stick to the facts. The observed number is NOT zero. E.g., the second last ICQC (Helsinki 2009) had lectures by Odile Eisenstein, Leticia Gonzáles, Emily A. Carter (one of the three signers of the current petition), Claudia Filippi and Nancy Makri. Five is not zero. Last time (ICQC Boulder 2012), there were Giulia Galli, Barbara Kirchner and Vlasta Bonacić-Koutecký. Three is not zero. [I'm not touching the issue of what is the correct amount per gender.] -- --------------------------------------------------------------- Mr. Susi Lehtola, PhD Research Associate susi.lehtola]*[alumni.helsinki.fi Department of Applied Physics http://www.helsinki.fi/~jzlehtol Aalto University Finland --------------------------------------------------------------- Susi Lehtola, FT Tutkijatohtori susi.lehtola]*[alumni.helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Aalto-yliopisto --------------------------------------------------------------- From owner-chemistry@ccl.net Wed Feb 19 18:57:01 2014 From: "Fedor Goumans goumans ~~ scm.com" To: CCL Subject: CCL:G: GAUSSIAN/GAMESS/MOLPRO/CRYSTAL: different energies - f function basis Message-Id: <-49770-140219152548-31755-6FSp5qT5fshJ0OD9khptIQ=server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 19 Feb 2014 21:25:36 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans%scm.com] Dear Mike, Gaussian and CRYSTAL use Cartesian basis functions by default (i.e. 10 f-functions), while Molpro (and apparently GAMESS) use spherical basis functions by default (i.e. 7 f-functions) Because of the extra flexibility in the Cartesian f-functions (effectively 3 extra diffuse functions) you consistently find lower energies for those codes that use Cartesian functions by default. Check the documentation of the codes to see how you can switch the default behavior from pure/spherical functions to Cartesian or v.v. You can find a bit on the transformations here: http://theochem.github.io/horton/tut_gaussian_basis.html Hope this solves the mystery. Best wishes, Fedor On 2/19/2014 6:30 PM, Mike Towler mdt26-.-cam.ac.uk wrote: > Sent to CCL by: "Mike Towler" [mdt26*cam.ac.uk] > Hello, > > I'm one of the authors of the CASINO program - a widely-used quantum Monte > Carlo code: http://vallico.net/casinoqmc/ . The way QMC works, CASINO > reads a 'trial wave function' generated by an external code using e.g. a > Hartree-Fock or a DFT calculation, and then it proceeds to 'improve the > answer' (details irrelevant). I'm therefore responsible for maintaining > interfaces between CASINO and other people's software - a list of the > fifteen codes we supposedly support is here: > > http://vallico.net/casinoqmc/interfaces > > For the purposes of my present question, this list includes GAUSSIAN, > GAMESS, CRYSTAL, and MOLPRO. > > I've recently started a formal check of the way these interfaces handle > higher angular momentum Gaussian functions (by which I mean f and g along > with d for completeness). The complexity of the expressions and the > different conventions in use mean that this sort of thing is very easy to > screw up. > > Basic checks are simple enough, since (1) CASINO does a numerical check of > its own analytic derivatives (it needs the value of the orbitals, the > gradient, and the Laplacian at random points in configuration space), and > (2) CASINO is capable of running in pure Hartree-Fock mode, and thus > through Monte Carlo numerical integration it should be able to give the > same Hartree-Fock energy (within statistical error bars) as the code that > generated the trial wave function. > > To check the different angular momenta individually, I've created a set of > three input files for the methane molecule, with only d functions in the > basis, only f functions, and only g functions (let's call them 'd-ane', > 'f-ane', and 'g-ane'). > > However, before we even get to CASINO, and looking first at f-ane, we've > found that the four codes above give very different answers for the > Hartree-Fock energy. In fact GAUSSIAN and CRYSTAL give -11.3966 au, but > both GAMESS and MOLPRO give -11.2286 au. > > (For the record, CASINO agrees with GAUSSIAN and CRYSTAL for the HF energy > when fed with their trial wave functions. It's not been possible to check > with GAMESS and MOLPRO as their current interfaces to CASINO don't yet > support f functions.. though they will shortly.) > > Now I don't have the experience or any access to any of these codes apart >> from CRYSTAL (I got some kind colleagues to run the calculations for me), > so it's difficult for me to see why this difference exists, and my > colleagues aren't sure either. There was some suggestion that it might be > to do with the spherical/Cartesian basis set conversion? So I was > wondering, are there any GAMESS, GAUSSIAN, or MOLPRO gurus out there who > can shed any light on this problem? It seems strange that such well-known > codes would give such different answers for such a simple system. > > The input files for the four codes are here: > > http://www.tcm.phy.cam.ac.uk/~mdt26/g/crystal.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/gamess.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/gaussian.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro1.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro2.txt > > Any assistance will be gratefully appreciated. > > Thanks, > Mike Towler> > -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans[a]scm.com http://www.scm.com From owner-chemistry@ccl.net Wed Feb 19 19:32:00 2014 From: "Raghu R raghu.rama.chem###gmail.com" To: CCL Subject: CCL:G: GAUSSIAN/GAMESS/MOLPRO/CRYSTAL: different energies - f function basis Message-Id: <-49771-140219160725-23978-SOUF4UOYovywegismmIGXQ(-)server.ccl.net> X-Original-From: Raghu R Content-Type: multipart/alternative; boundary=089e0158a9be0b084404f2c8c6f1 Date: Wed, 19 Feb 2014 22:07:16 +0100 MIME-Version: 1.0 Sent to CCL by: Raghu R [raghu.rama.chem. : .gmail.com] --089e0158a9be0b084404f2c8c6f1 Content-Type: text/plain; charset=ISO-8859-1 Hello Mike, Both Molpro and Gaussian seem to use pure spherical harmonics with your input. The issue is related to different set ups in to accelerate/aid the SCF convergence. I personally like the robust default convergence set up in one of the programs. To give a quick proof of principle, try running the same inputs with Charge = +2, you should get -10.91352852 Hartree using both Molpro and Gaussian. Best, Raghu Research Associate, University of Basel. On Wed, Feb 19, 2014 at 6:30 PM, Mike Towler mdt26-.-cam.ac.uk < owner-chemistry : ccl.net> wrote: > > Sent to CCL by: "Mike Towler" [mdt26*cam.ac.uk] > Hello, > > I'm one of the authors of the CASINO program - a widely-used quantum Monte > Carlo code: http://vallico.net/casinoqmc/ . The way QMC works, CASINO > reads a 'trial wave function' generated by an external code using e.g. a > Hartree-Fock or a DFT calculation, and then it proceeds to 'improve the > answer' (details irrelevant). I'm therefore responsible for maintaining > interfaces between CASINO and other people's software - a list of the > fifteen codes we supposedly support is here: > > http://vallico.net/casinoqmc/interfaces > > For the purposes of my present question, this list includes GAUSSIAN, > GAMESS, CRYSTAL, and MOLPRO. > > I've recently started a formal check of the way these interfaces handle > higher angular momentum Gaussian functions (by which I mean f and g along > with d for completeness). The complexity of the expressions and the > different conventions in use mean that this sort of thing is very easy to > screw up. > > Basic checks are simple enough, since (1) CASINO does a numerical check of > its own analytic derivatives (it needs the value of the orbitals, the > gradient, and the Laplacian at random points in configuration space), and > (2) CASINO is capable of running in pure Hartree-Fock mode, and thus > through Monte Carlo numerical integration it should be able to give the > same Hartree-Fock energy (within statistical error bars) as the code that > generated the trial wave function. > > To check the different angular momenta individually, I've created a set of > three input files for the methane molecule, with only d functions in the > basis, only f functions, and only g functions (let's call them 'd-ane', > 'f-ane', and 'g-ane'). > > However, before we even get to CASINO, and looking first at f-ane, we've > found that the four codes above give very different answers for the > Hartree-Fock energy. In fact GAUSSIAN and CRYSTAL give -11.3966 au, but > both GAMESS and MOLPRO give -11.2286 au. > > (For the record, CASINO agrees with GAUSSIAN and CRYSTAL for the HF energy > when fed with their trial wave functions. It's not been possible to check > with GAMESS and MOLPRO as their current interfaces to CASINO don't yet > support f functions.. though they will shortly.) > > Now I don't have the experience or any access to any of these codes apart > > from CRYSTAL (I got some kind colleagues to run the calculations for me), > so it's difficult for me to see why this difference exists, and my > colleagues aren't sure either. There was some suggestion that it might be > to do with the spherical/Cartesian basis set conversion? So I was > wondering, are there any GAMESS, GAUSSIAN, or MOLPRO gurus out there who > can shed any light on this problem? It seems strange that such well-known > codes would give such different answers for such a simple system. > > The input files for the four codes are here: > > http://www.tcm.phy.cam.ac.uk/~mdt26/g/crystal.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/gamess.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/gaussian.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro1.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro2.txt > > Any assistance will be gratefully appreciated. > > Thanks, > Mike Towler> > > --089e0158a9be0b084404f2c8c6f1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello Mike,

Both Molpro and Gaussian seem to use= pure spherical harmonics with your input.

The issue is related to different set ups in to accelerate/aid the SCF conv= ergence. I personally like the robust default convergence set up in one of = the programs.

To give a quick proof of principle, try running the same inputs with Charge= =3D +2, you should get -10.91352852 Hartree using both Molpro and Gaussian= .

Best,
Raghu

Research Associate,
University of Basel.










On Wed, Feb 19, 2014 at 6:30 PM, Mike Towler mdt26-.-cam.ac.uk <owner-chemistry : ccl.net&g= t; wrote:

Sent to CCL by: "Mike =A0Towler" [mdt26*cam.ac.uk]
Hello,

I'm one of the authors of the CASINO program - a widely-used quantum Mo= nte
Carlo code: htt= p://vallico.net/casinoqmc/ . The way QMC works, CASINO
reads a 'trial wave function' generated by an external code using e= .g. a
Hartree-Fock or a DFT calculation, and then it proceeds to 'improve the=
answer' (details irrelevant). I'm therefore responsible for maintai= ning
interfaces between CASINO and other people's software - a list of the fifteen codes we supposedly support is here:

http:= //vallico.net/casinoqmc/interfaces

For the purposes of my present question, this list includes GAUSSIAN,
GAMESS, CRYSTAL, and MOLPRO.

I've recently started a formal check of the way these interfaces handle=
higher angular momentum Gaussian functions (by which I mean f and g along with d for completeness). The complexity of the expressions and the
different conventions in use mean that this sort of thing is very easy to screw up.

Basic checks are simple enough, since (1) CASINO does a numerical check of<= br> its own analytic derivatives (it needs the value of the orbitals, the
gradient, and the Laplacian at random points in configuration space), and (2) CASINO is capable of running in pure Hartree-Fock mode, and thus
through Monte Carlo numerical integration it should be able to give the
same Hartree-Fock energy (within statistical error bars) as the code that generated the trial wave function.

To check the different angular momenta individually, I've created a set= of
three input files for the methane molecule, with only d functions in the basis, only f functions, and only g functions (let's call them 'd-a= ne',
'f-ane', and 'g-ane').

However, before we even get to CASINO, and looking first at f-ane, we'v= e
found that the four codes above give very different answers for the
Hartree-Fock energy. In fact GAUSSIAN and CRYSTAL give -11.3966 au, but
both GAMESS and MOLPRO give -11.2286 au.

(For the record, CASINO agrees with GAUSSIAN and CRYSTAL for the HF energy<= br> when fed with their trial wave functions. It's not been possible to che= ck
with GAMESS and MOLPRO as their current interfaces to CASINO don't yet<= br> support f functions.. though they will shortly.)

Now I don't have the experience or any access to any of these codes apa= rt
> from CRYSTAL (I got some kind colleagues to run the calculations for m= e),
so it's difficult for me to see why this difference exists, and my
colleagues aren't sure either. There was some suggestion that it might = be
to do with the spherical/Cartesian basis set conversion? =A0So I was
wondering, are there any GAMESS, GAUSSIAN, or MOLPRO gurus out there who can shed any light on this problem? It seems strange that such well-known codes would give such different answers for such a simple system.

The input files for the four codes are here:

http://www.tcm.phy.cam.ac.uk/~mdt26/g/crystal.txt
http://www.tcm.phy.cam.ac.uk/~mdt26/g/gamess.txt
http://www.tcm.phy.cam.ac.uk/~mdt26/g/gaussian.txt
http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro1.txt
http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro2.txt

Any assistance will be gratefully appreciated.

Thanks,
Mike Towler



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--089e0158a9be0b084404f2c8c6f1-- From owner-chemistry@ccl.net Wed Feb 19 20:27:00 2014 From: "Matthias Heger mheger_+_gwdg.de" To: CCL Subject: CCL:G: GAUSSIAN/GAMESS/MOLPRO/CRYSTAL: different energies - f function basis Message-Id: <-49772-140219175621-17941-NBZxECVtJgh6eQ7h2GwBpQ|server.ccl.net> X-Original-From: Matthias Heger Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Wed, 19 Feb 2014 23:56:08 +0100 MIME-Version: 1.0 Sent to CCL by: Matthias Heger [mheger ~ gwdg.de] Even if your problem is not about the use of Cartesian or spherical functions (as the other answers suggest), I'd just like to add that the simplest way to check for inconsistencies between your calculations would be to take a look at our outputs and see if the number of basis functions differ. I think Gaussian also supplies some keywords to use either construction, so if you're bored you could just try to switch between them and see what happens. Am 19-02-2014 18:30, schrieb Mike Towler mdt26-.-cam.ac.uk: > > Sent to CCL by: "Mike Towler" [mdt26*cam.ac.uk] > Hello, > > I'm one of the authors of the CASINO program - a widely-used quantum Monte > Carlo code: http://vallico.net/casinoqmc/ . The way QMC works, CASINO > reads a 'trial wave function' generated by an external code using e.g. a > Hartree-Fock or a DFT calculation, and then it proceeds to 'improve the > answer' (details irrelevant). I'm therefore responsible for maintaining > interfaces between CASINO and other people's software - a list of the > fifteen codes we supposedly support is here: > > http://vallico.net/casinoqmc/interfaces > > For the purposes of my present question, this list includes GAUSSIAN, > GAMESS, CRYSTAL, and MOLPRO. > > I've recently started a formal check of the way these interfaces handle > higher angular momentum Gaussian functions (by which I mean f and g along > with d for completeness). The complexity of the expressions and the > different conventions in use mean that this sort of thing is very easy to > screw up. > > Basic checks are simple enough, since (1) CASINO does a numerical check of > its own analytic derivatives (it needs the value of the orbitals, the > gradient, and the Laplacian at random points in configuration space), and > (2) CASINO is capable of running in pure Hartree-Fock mode, and thus > through Monte Carlo numerical integration it should be able to give the > same Hartree-Fock energy (within statistical error bars) as the code that > generated the trial wave function. > > To check the different angular momenta individually, I've created a set of > three input files for the methane molecule, with only d functions in the > basis, only f functions, and only g functions (let's call them 'd-ane', > 'f-ane', and 'g-ane'). > > However, before we even get to CASINO, and looking first at f-ane, we've > found that the four codes above give very different answers for the > Hartree-Fock energy. In fact GAUSSIAN and CRYSTAL give -11.3966 au, but > both GAMESS and MOLPRO give -11.2286 au. > > (For the record, CASINO agrees with GAUSSIAN and CRYSTAL for the HF energy > when fed with their trial wave functions. It's not been possible to check > with GAMESS and MOLPRO as their current interfaces to CASINO don't yet > support f functions.. though they will shortly.) > > Now I don't have the experience or any access to any of these codes apart >> from CRYSTAL (I got some kind colleagues to run the calculations for me), > so it's difficult for me to see why this difference exists, and my > colleagues aren't sure either. There was some suggestion that it might be > to do with the spherical/Cartesian basis set conversion? So I was > wondering, are there any GAMESS, GAUSSIAN, or MOLPRO gurus out there who > can shed any light on this problem? It seems strange that such well-known > codes would give such different answers for such a simple system. > > The input files for the four codes are here: > > http://www.tcm.phy.cam.ac.uk/~mdt26/g/crystal.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/gamess.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/gaussian.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro1.txt > http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro2.txt > > Any assistance will be gratefully appreciated. > > Thanks, > Mike Towler> > From owner-chemistry@ccl.net Wed Feb 19 21:02:00 2014 From: "Salter-Duke, Brian James - brian.james.duke###gmail.com" To: CCL Subject: CCL:G: GAUSSIAN/GAMESS/MOLPRO/CRYSTAL: different energies - f function basis Message-Id: <-49773-140219181010-31091-KTWeCEcyTYKQHmSNpsfPnA_-_server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 20 Feb 2014 10:09:56 +1100 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke{=}gmail.com] On Wed, Feb 19, 2014 at 09:57:38PM +0200, Susi Lehtola susi.lehtola[#]alumni.helsinki.fi wrote: > > Sent to CCL by: Susi Lehtola [susi.lehtola.-$-.alumni.helsinki.fi] > On Wed, 19 Feb 2014 12:30:08 -0500 > "Mike Towler mdt26-.-cam.ac.uk" wrote: > > To check the different angular momenta individually, I've created a set of > > three input files for the methane molecule, with only d functions in the > > basis, only f functions, and only g functions (let's call them 'd-ane', > > 'f-ane', and 'g-ane'). > > > > However, before we even get to CASINO, and looking first at f-ane, we've > > found that the four codes above give very different answers for the > > Hartree-Fock energy. In fact GAUSSIAN and CRYSTAL give -11.3966 au, but > > both GAMESS and MOLPRO give -11.2286 au. > > > > Now I don't have the experience or any access to any of these codes apart > > > from CRYSTAL (I got some kind colleagues to run the calculations for me), > > so it's difficult for me to see why this difference exists, and my > > colleagues aren't sure either. There was some suggestion that it might be > > to do with the spherical/Cartesian basis set conversion? So I was > > wondering, are there any GAMESS, GAUSSIAN, or MOLPRO gurus out there who > > can shed any light on this problem? It seems strange that such well-known > > codes would give such different answers for such a simple system. > > There's no problem here. I checked the GAUSSIAN result, and indeed I get > the same energy -11.3966 au. I ran the test also with ERKALE, which > gives -11.2286 au. So there is something odd here. > > However, if you put in Guess=Core into the Gaussian run, you'll > converge to -11.2286 au. > > The reason why you get two different energies is that the runs converge > to different solutions. > > If you run an optimizing stability analysis (Stable=(Opt,RRHF) in > Gaussian for spin-restricted analysis), you'll see that the -11.2286 au. > solution is a saddle point, and that the local minimum the program will > converge into has energy -11.3966 au. A good analysis. However, the lower result of -11.3966 au does not have orbitals that reflect the tetrahedral symmetry. The 5 occupied orbital energies are -3.09417, -0.50018, 2 x -0.,49114. The higher result in GAMESS has -3.1154 and 3 x -0.5128. The conclusion - you are using a very poor choice of basis set, but anyone can see that. Brian. > -- > --------------------------------------------------------------- > Mr. Susi Lehtola, PhD Research Associate > susi.lehtola__alumni.helsinki.fi Department of Applied Physics > http://www.helsinki.fi/~jzlehtol Aalto University > Finland > --------------------------------------------------------------- > Susi Lehtola, FT Tutkijatohtori > susi.lehtola__alumni.helsinki.fi Fysiikan laitos > http://www.helsinki.fi/~jzlehtol Aalto-yliopisto > ---------------------------------------------------------------> -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke-$-monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia From owner-chemistry@ccl.net Wed Feb 19 21:36:00 2014 From: "Salter-Duke, Brian James - brian.james.duke.\a/.gmail.com" To: CCL Subject: CCL:G: GAUSSIAN/GAMESS/MOLPRO/CRYSTAL: different energies - f function basis Message-Id: <-49774-140219210249-20176-Tb3yxJhXmiDvgMcwwE9yPw\a/server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 20 Feb 2014 13:02:24 +1100 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke===gmail.com] On Wed, Feb 19, 2014 at 09:25:36PM +0100, Fedor Goumans goumans ~~ scm.com wrote: > > Sent to CCL by: Fedor Goumans [goumans%scm.com] > Dear Mike, > > Gaussian and CRYSTAL use Cartesian basis functions by default (i.e. > 10 f-functions), while Molpro (and apparently GAMESS) use spherical > basis functions by default (i.e. 7 f-functions) This is not correct and it needs to be clarified. GAMESS always uses cartesian functions, so in this case there are 210 basis functions. If ISPHER=1 in $CONTRL, as in this case, the calculation gives the spherical harmonic result by removing many virtual orbitals ( in this case the 3 extra p functions per f shell), so there are only 147 MOs. GAMESS results are always expressed over the cartesian basis set, even when the result is the spherical harmonic result. The Gaussian run is using spherical harmonics, so there are 147 basis functions and 147 MOs. None of the energies given are cartesian basis energies. The explanation for the difference has been given earlier. Brian. > Because of the extra flexibility in the Cartesian f-functions > (effectively 3 extra diffuse functions) you consistently find lower > energies for those codes that use Cartesian functions by default. > Check the documentation of the codes to see how you can switch the > default behavior from pure/spherical functions to Cartesian or v.v. > > You can find a bit on the transformations here: > http://theochem.github.io/horton/tut_gaussian_basis.html > > Hope this solves the mystery. > > Best wishes, > Fedor > > On 2/19/2014 6:30 PM, Mike Towler mdt26-.-cam.ac.uk wrote: > >Sent to CCL by: "Mike Towler" [mdt26*cam.ac.uk] > >Hello, > > > >I'm one of the authors of the CASINO program - a widely-used quantum Monte > >Carlo code: http://vallico.net/casinoqmc/ . The way QMC works, CASINO > >reads a 'trial wave function' generated by an external code using e.g. a > >Hartree-Fock or a DFT calculation, and then it proceeds to 'improve the > >answer' (details irrelevant). I'm therefore responsible for maintaining > >interfaces between CASINO and other people's software - a list of the > >fifteen codes we supposedly support is here: > > > >http://vallico.net/casinoqmc/interfaces > > > >For the purposes of my present question, this list includes GAUSSIAN, > >GAMESS, CRYSTAL, and MOLPRO. > > > >I've recently started a formal check of the way these interfaces handle > >higher angular momentum Gaussian functions (by which I mean f and g along > >with d for completeness). The complexity of the expressions and the > >different conventions in use mean that this sort of thing is very easy to > >screw up. > > > >Basic checks are simple enough, since (1) CASINO does a numerical check of > >its own analytic derivatives (it needs the value of the orbitals, the > >gradient, and the Laplacian at random points in configuration space), and > >(2) CASINO is capable of running in pure Hartree-Fock mode, and thus > >through Monte Carlo numerical integration it should be able to give the > >same Hartree-Fock energy (within statistical error bars) as the code that > >generated the trial wave function. > > > >To check the different angular momenta individually, I've created a set of > >three input files for the methane molecule, with only d functions in the > >basis, only f functions, and only g functions (let's call them 'd-ane', > >'f-ane', and 'g-ane'). > > > >However, before we even get to CASINO, and looking first at f-ane, we've > >found that the four codes above give very different answers for the > >Hartree-Fock energy. In fact GAUSSIAN and CRYSTAL give -11.3966 au, but > >both GAMESS and MOLPRO give -11.2286 au. > > > >(For the record, CASINO agrees with GAUSSIAN and CRYSTAL for the HF energy > >when fed with their trial wave functions. It's not been possible to check > >with GAMESS and MOLPRO as their current interfaces to CASINO don't yet > >support f functions.. though they will shortly.) > > > >Now I don't have the experience or any access to any of these codes apart > >>from CRYSTAL (I got some kind colleagues to run the calculations for me), > >so it's difficult for me to see why this difference exists, and my > >colleagues aren't sure either. There was some suggestion that it might be > >to do with the spherical/Cartesian basis set conversion? So I was > >wondering, are there any GAMESS, GAUSSIAN, or MOLPRO gurus out there who > >can shed any light on this problem? It seems strange that such well-known > >codes would give such different answers for such a simple system. > > > >The input files for the four codes are here: > > > >http://www.tcm.phy.cam.ac.uk/~mdt26/g/crystal.txt > >http://www.tcm.phy.cam.ac.uk/~mdt26/g/gamess.txt > >http://www.tcm.phy.cam.ac.uk/~mdt26/g/gaussian.txt > >http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro1.txt > >http://www.tcm.phy.cam.ac.uk/~mdt26/g/molpro2.txt > > > >Any assistance will be gratefully appreciated. > > > >Thanks, > >Mike Towler> > > > > > -- > Dr. T. P. M. (Fedor) Goumans > Business Developer > Scientific Computing & Modelling NV (SCM) > Vrije Universiteit, FEW, Theoretical Chemistry > De Boelelaan 1083 > 1081 HV Amsterdam, The Netherlands > T +31 20 598 7625 > F +31 20 598 7629 > E-mail: goumans_-_scm.com > http://www.scm.comConferences: > http://server.ccl.net/chemistry/announcements/conferences/> -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke]~[monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia