From owner-chemistry@ccl.net Sun Aug 31 05:14:01 2008 From: "Orlin Blajiev blajiev-*-vub.ac.be" To: CCL Subject: CCL:G: APT And Mulliken Message-Id: <-37683-080831051046-27743-ZDRgxfoWN6hCff7mniSEug.@.server.ccl.net> X-Original-From: Orlin Blajiev Date: Sun, 31 Aug 2008 11:10:23 +0200 (CEST) Sent to CCL by: Orlin Blajiev [blajiev,,vub.ac.be] Hi everybody, I have a system which I charge and discharge by adding or subtracting electrons. Then when I looked at the output I saw that the total number of electrons is correctly given by the Mulliken approach and was not so by the APT. For example two electrons out, then: Sum of Mulliken charges= 2.00000 But Sum of APT charges= 2.14530 Can someone tell me why APT charge is not an integer one? Thanks. Orlin >Sent to CCL by: frisch^_^gaussian.com (Michael Frisch) >On Wed, Jun 18, 2008 at 02:17:41PM -0400, Steve Williams willsd]|[appstate.edu wrote: >> >> Sent to CCL by: Steve Williams [willsd^_^appstate.edu] >> Raman intensities are available in G03, but since they require numerical >> derivatives for MP2 and DFT methods they are very slow to compute and by >> default they are not calculated on a frequency job. If you change your >> input to include freq=raman on the route line, they will be computed. >> Six separate calculations will be done for each atom (+/- displacements >> in x, y, z) to compute the needed polarizability derivatives. You can >> estimate how long this will take by doing a single point polarizability >> calculation then multiplying the time required for this by 6*N where N >> is the number of atoms in your molecule (the portion you want to compute >> with b3lyp). >> > >This is not correct. In G03, MP2 and B3LYP Raman intensities (static >polarizability derivatives, "Freq=Raman" on the route card) are done >by numerically differentiating the analytic dipole derivatives with >respect to an applied electric field. So there are only 6 additional >calculations regardless of the size of the molecule. The cost of each >of the 6 calculations in a finite electric field is somewhat more than >a polarizability calculation but much less than the calculation of the >second derivatives for the basic frequency calculation. So for very >small molecules the total cost of Freq=Raman with DFT or MP2 is around >than 3x the cost of just doing Freq, but this drops to 1.5x for larger >systems. > >Freq=Raman does work with ONIOM. With ONIOM(MO:MM) and mechanical >embedding the cost is about the same as for the MO calculation on the >model system. With ONIOM(MO:MM) and electronic embedding, the cost is >higher than just doing the model system (with or without Raman) >because derivatives with respect to all the nuclei have to be included >in the QM calculation. > >Mike Frisch> > > > Orlin Blajiev Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium http://www.vub.ac.be/META/ tel.: 32-(0)2-6293538 fax : 32-(0)2-6293200 From owner-chemistry@ccl.net Sun Aug 31 06:25:01 2008 From: "Marcel Swart marcel.swart++icrea.es" To: CCL Subject: CCL: Minima Message-Id: <-37684-080831061858-9273-AIhF2efcaSuyWuUVhGDxwg^^server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-7--797240484 Date: Sun, 31 Aug 2008 11:40:11 +0200 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Marcel Swart [marcel.swart ~ icrea.es] --Apple-Mail-7--797240484 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Yes, there are indeed different minima, which are characterized by =20 all positive frequencies, if they are well separated from each other. For instance, taking as =20 an example the bimolecular nucleophilic substitution (Sn2) reaction, between Cl(-) + CH3Br =3D> CH3Cl + Br(-). In this reaction (in the gas-phase !), there are several minima: reactants, reactant-complex, product-complex, products. (note that I mean here the reactants and products at infinite =20 separation) It is fairly easy to distinguish between them, and draw an energy profile for this reaction (see e.g. J.Comput.Chem. 2007, 28, 1551 and references therein). Note that these minima are connected along the energy profile by the backside pathway reaction coordinate. (You might check this with IRC calculations) Note that for the abovementioned reaction, the product complex is lowest in energy, e.g. the global minimum along the Sn2 pathway. However, sometimes there are also competing pathways, e.g. substitution vs. elimination, in which case you obtain minima along either (or both) pathways. See e.g. Bento, A. P.; Sol=E0, M.; Bickelhaupt, F. M. J. Chem. Theor. Comp. =20 2008, 4, 929-940 Hope this helps. Marcel. On Aug 29, 2008, at 7:07 PM, Neelum Seeburrun nseeburrun**gmail.com =20 wrote: > > Sent to CCL by: "Neelum Seeburrun" [nseeburrun!=3D!gmail.com] > Dear All > The problem I am having is that there are different types of =20 > minima: local,global,true and genuine. All of the minima give real =20 > values of vibrational frequencies. So how to distingush between them? > Your help or references will be appreciated. > Neelum > nseeburrun ~~ gmail.com > > > > -=3D This is automatically added to each message by the mailing =20 > script =3D- > To recover the email address of the author of the message, please =20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: =20 > search)> > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart^^icrea.es marcel.swart^^udg.edu web http://www.icrea.es/pag.asp?id=3DMarcel.Swart http://iqc.udg.edu/~marcel =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --Apple-Mail-7--797240484 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Yes, there are indeed different minima, which are characterized by all = positive=A0frequencies,
if they are well separated from each other. = For instance, taking as an example = the
bimolecular=A0nucleophilic substitution (Sn2) reaction, = between
Cl(-) + CH3Br =3D> CH3Cl + Br(-).
In this = reaction (in the gas-phase !), there are several = minima:=A0
reactants, reactant-complex, product-complex, = products.
(note that I mean here the reactants and = products at infinite separation)
It is fairly easy to = distinguish between them, and draw an energy
profile for this = reaction (see e.g. J.Comput.Chem. 2007, 28, 1551 = and
references therein).

Note that = these minima are connected along the energy profile by = the
backside pathway reaction coordinate. (You might check = this with IRC
calculations)

Note that = for the abovementioned reaction, the product complex is
lowest = in energy, e.g. the global minimum along the Sn2 = pathway.
However, sometimes there are also competing pathways, = e.g.=A0
substitution vs. elimination, in which case you obtain = minima along
either (or both) pathways. See = e.g.=A0
Bento, A. P.; Sol=E0, M.; Bickelhaupt, F. M. J. = Chem. Theor. Comp. 2008, 4, 929-940

Hope this = helps.

Marcel.
On Aug = 29, 2008, at 7:07 PM, Neelum Seeburrun nseeburrun**gmail.com = wrote:


Sent to CCL by: "Neelum=A0 Seeburrun" = [nseeburrun!=3D!gmail.com]
Dear = All
The problem I am having is that = there are different types of minima: local,global,true and genuine. All = of the minima give real values of vibrational frequencies. So how to = distingush between them?
Your help or = references will be appreciated.
nseeburrun ~~ = gmail.com



-=3D This is = automatically added to each message by the mailing script =3D-
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the strange characters on = the top line to the ^^ sign. You can also
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If your mail bounces from CCL with 5.7.1 error, = check:




dr. Marcel = Swart

ICREA = researcher=A0at
Institut de Qu=EDmica = Computacional
Universitat de = Girona

Parc Cient=EDfic i = Tecnol=F2gic
Pic de Peguera = 15
Catalunya = (Spain)

tel
http://iqc.udg.edu/~marcel<= /span>



= --Apple-Mail-7--797240484-- From owner-chemistry@ccl.net Sun Aug 31 07:49:00 2008 From: "Mr Shabbir shabbir!=!nenu.edu.cn" To: CCL Subject: CCL: Easy convergence of Diffuse functions Message-Id: <-37685-080831074200-8901-+WSWHe8948LaxGxHYwkEqg() server.ccl.net> X-Original-From: "Mr Shabbir" Date: Sun, 31 Aug 2008 07:41:56 -0400 Sent to CCL by: "Mr Shabbir" [shabbir]^[nenu.edu.cn] Dear all I want to share some thing about optimization. I optimized several systems with 6-31G* basis set but when I use diffuse function (+) the same previously optimized system at (6-31G*) fails to converge by using diffuse function. How to treat the diffuse function especially in optimization? Is there any special keyword or way that can make the convergence easy with diffuse functions? Regards Mr.Shabbir shabbir_._nenu.edu.cn From owner-chemistry@ccl.net Sun Aug 31 13:19:01 2008 From: "errol lewars elewars-*-trentu.ca" To: CCL Subject: CCL: Easy convergence of Diffuse functions Message-Id: <-37686-080831123523-29727-XQgbHFkI4CAcusvWbDmiOg|,|server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 31 Aug 2008 12:35:13 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars%trentu.ca] 2008 Aug 31 Convergence problems with diffuse functions is a well-known phenomenon. You could try getting a wavefunction with, say, the 6-31G* basis then using that wavefunction as an initial guess for a 6-31+G* job. The keyword for taking the previous wavefunction as your guess depends on your program. E. Lewars === Mr Shabbir shabbir!=!nenu.edu.cn wrote: >Sent to CCL by: "Mr Shabbir" [shabbir]^[nenu.edu.cn] >Dear all >I want to share some thing about optimization. I optimized several systems with 6-31G* basis set but when I use diffuse function (+) the same previously optimized system at (6-31G*) fails to converge by using diffuse function. How to treat the diffuse function especially in optimization? Is there any special keyword or way that can make the convergence easy with diffuse functions? >Regards >Mr.Shabbir >shabbir::nenu.edu.cn> > > > From owner-chemistry@ccl.net Sun Aug 31 13:53:00 2008 From: "Fu-Ming Ying fmying * gmail.com" To: CCL Subject: CCL: Pure vs. Cartesian Basis Functions Message-Id: <-37687-080829101538-28868-fP2ARbDalyuVwuscDc1M5Q!A!server.ccl.net> X-Original-From: Fu-Ming Ying Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Fri, 29 Aug 2008 15:00:39 +0200 MIME-Version: 1.0 Sent to CCL by: Fu-Ming Ying [fmying||gmail.com] hej I don' think the result will differ much for geometry optimization. But if you'd better use the same type during all the calculations. For example, if you use 5D in hf/3-21G, then I think it's better to use 5D in b3lyp/6-31++G(D,P) etc. gnli gnli,dicp.ac.cn wrote: > > *Dear CCLer,* > > *Please forgive me for my simple question.* > > *Is it necessary to keep the basis set to be Pure or Cartesian type > during all the calculate step in one system?* > > *For example, we optimize a molecule using “hf/3-21g hf/6-31g > b3lyp/6-31g b3lyp/6-31++g(d,p) b3lyp/aug-cc-pvdz” gradually, need we > define the Basis Functions all in 5D 7F or 6D 10F in the route section > consistently, or just using default? Is the difference serious? * > > *Thanks!* > > best wishes > Guanna Li > gnli]|[dicp.ac.cn > > > -- Fuming Ying Theoretical Chemistry, KTH AlbaNova University Center 106 91 Stockholm, Sweden From owner-chemistry@ccl.net Sun Aug 31 16:18:00 2008 From: "Cesar Millan pachequin^^gmail.com" To: CCL Subject: CCL: DNA base pair step parameters from DCD trajectory Message-Id: <-37688-080831161637-14230-K1J6JHArQCqeuyhkWBCMAQ*o*server.ccl.net> X-Original-From: "Cesar Millan" Date: Sun, 31 Aug 2008 16:16:33 -0400 Sent to CCL by: "Cesar Millan" [pachequin#gmail.com] Hi everyone, I want to analyze a DNA trajectory generated by NAMD and obtain the different base pair step parameters for each frame (shift, rise, roll, etc). I used to do this using Dials and Windows but it does not work in Linux based machines. Does anyone knows any software running in linux that I could use to do this analysis? Thank you in advance Cesar From owner-chemistry@ccl.net Sun Aug 31 18:11:01 2008 From: "David Hose anthrax_brothers*hotmail.com" To: CCL Subject: CCL:G: Easy convergence of Diffuse functions Message-Id: <-37689-080831180933-16680-7WkurxNLOk0pQmSFRb52Yg+/-server.ccl.net> X-Original-From: "David Hose" Date: Sun, 31 Aug 2008 18:09:30 -0400 Sent to CCL by: "David Hose" [anthrax_brothers:hotmail.com] Hi Ya, The addition of diffuse functions to the basis set is well known to cause problems with the convergence of the calculations. The most common fix is to use a better quality guess for the initial wavefunction in the second calculation. Assuming that you are using Gaussian, the simplest way is to optimise the geometry of the molecule at say HF/6-31G* level of theory. Duplicate the resulting checkpoint point file. Then set up the second (single point?) calculation, at say the HF/6-31+G* level of theory, with Guess=Checkpoint included in the route selection, ensuring that the %chk points to the previous calculation checkpoint file. On occasions, it is better if the previous calculation included a frequency calculation as the superior hessian allows the subsequent calculation converge more easily. There are some other approaches that can be used for difficult cases, but the above method typically works. I suggest that you check out David Young's book Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems. A great source of handy hints and tips. There is a version of his book here on CCL. The section of converge can be found here. http://www.ccl.net/cca/documents/dyoung/topics-orig/converge.html Regards, Dave. _____________ Sent to CCL by: "Mr Shabbir" [shabbir]^[nenu.edu.cn] Dear all I want to share some thing about optimization. I optimized several systems with 6-31G* basis set but when I use diffuse function (+) the same previously optimized system at (6-31G*) fails to converge by using diffuse function. How to treat the diffuse function especially in optimization? Is there any special keyword or way that can make the convergence easy with diffuse functions? Regards Mr.Shabbir shabbir::nenu.edu.cn From owner-chemistry@ccl.net Sun Aug 31 22:45:00 2008 From: "Brian Salter-Duke brian.james.duke|a|gmail.com" To: CCL Subject: CCL:G: Pure vs. Cartesian Basis Functions Message-Id: <-37690-080831214413-14923-taquGaRCuZgQZdOp2wtNPA^_^server.ccl.net> X-Original-From: Brian Salter-Duke Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 01 Sep 2008 11:43:52 +1000 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke\a/gmail.com] Fu-Ming Ying fmying * gmail.com wrote: > > Sent to CCL by: Fu-Ming Ying [fmying||gmail.com] > > hej > I don' think the result will differ much for geometry optimization. > But if you'd better use the same type during all the calculations. > For example, if you use 5D in hf/3-21G, then I think it's better to use > 5D in b3lyp/6-31++G(D,P) etc. I think this misses the point. You should use the appropriate type that the basis set is defined for. Look at the defined defaults in the manual - pg 27 for G03 manual. 3-21G and 6-31G use 6D, while 6-311G uses 5D. If you go from 6-31G to 6-311G you should stick to the defaults, changing > from 6D to 5D. Brian. > gnli gnli,dicp.ac.cn wrote: >> >> *Dear CCLer,* >> >> *Please forgive me for my simple question.* >> >> *Is it necessary to keep the basis set to be Pure or Cartesian type >> during all the calculate step in one system?* >> >> *For example, we optimize a molecule using “hf/3-21g hf/6-31g >> b3lyp/6-31g b3lyp/6-31++g(d,p) b3lyp/aug-cc-pvdz” gradually, need we >> define the Basis Functions all in 5D 7F or 6D 10F in the route section >> consistently, or just using default? Is the difference serious? * >> >> *Thanks!* >> >> best wishes >> Guanna Li >> gnli]|[dicp.ac.cn >> -- Brian Salter-Duke (Brian Duke) Brian.James.Duke(a)gmail.com Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia http://www.salter-duke.bigpondhosting.com/brian/index.htm Honorary Researcher Fellow, Monash Institute of Pharmaceutical Sciences