From owner-chemistry@ccl.net Thu May 14 04:14:00 2009 From: "Mi yang shabbir3790,+,hotmail.com" To: CCL Subject: CCL:G: Dioxane in PCM with G03 Message-Id: <-39319-090514041106-31473-lFz5rIvY5Yc2UhtpVY6OjQ^-^server.ccl.net> X-Original-From: "Mi yang" Date: Thu, 14 May 2009 04:11:02 -0400 Sent to CCL by: "Mi yang" [shabbir3790-#-hotmail.com] Hello CCL user, Because my experiment data of polarizability is in Dioxane so I want to calculate polarizability in a Dioxane (Dielectric constant=2.22) with PCM method but this is not available in G03. 1- Can I calculate polarizability by specifying the dielectric constant of 2.22 with read option in input or some other way to do this? 2- If I choose a solvent (CCL4, dielectric constant= 2.228) which has dielectric constant near to Dioxane does it make sense? thanks Mi From owner-chemistry@ccl.net Thu May 14 04:49:00 2009 From: "Alcides Simao alsimao^-^gmail.com" To: CCL Subject: CCL:G: Dioxane in PCM with G03 Message-Id: <-39320-090514043756-25027-ntvk4sX+U8Gi8D2ZbVlWYw===server.ccl.net> X-Original-From: Alcides Simao Content-Type: multipart/alternative; boundary=0015174bdfd8c7bdf20469db3d36 Date: Thu, 14 May 2009 09:37:41 +0100 MIME-Version: 1.0 Sent to CCL by: Alcides Simao [alsimao:-:gmail.com] --0015174bdfd8c7bdf20469db3d36 Content-Type: text/plain; charset=ISO-8859-7 Content-Transfer-Encoding: quoted-printable PCM methods are available in G03, if you read the manual carefully ( http://www.gaussian.com/g_ur/k_scrf.htm ) However, as stated in the Gaussian manual: 'We list the =E5 values here for convenience, but be aware it is only one of many internal parameters used t= o define solvents. Thus, simply changing the =E5 value will not define a new solvent properly.' So, using CCl4 will not work (if it works, its plain coincidence, not science!) In order to solve such problem, please read more about PCM methods in any undergrad computational chemistry book and gather the data needed to solve the problem! Best, Alcides --0015174bdfd8c7bdf20469db3d36 Content-Type: text/html; charset=ISO-8859-7 Content-Transfer-Encoding: quoted-printable PCM methods are available in G03, if you read the manual carefully ( http://www.gaussian.com/g_ur/= k_scrf.htm )

However, as stated in the Gaussian manual: 'We= =20 list the =E5 values here for convenience, but be aware it is only one of=20 many internal parameters used to define solvents. Thus, simply changing the= =E5=20 value will not define a new solvent properly.'

So, using CCl4 wi= ll not work (if it works, its plain coincidence, not science!)

In or= der to solve such problem, please read more about PCM methods in any underg= rad computational chemistry book and gather the data needed to solve the pr= oblem!

Best,

Alcides
--0015174bdfd8c7bdf20469db3d36-- From owner-chemistry@ccl.net Thu May 14 06:26:00 2009 From: "Mi Yang shabbir3790(a)hotmail.com" To: CCL Subject: CCL:G: Dioxane in PCM with G03 Message-Id: <-39321-090514062411-17456-3dj57W49Xcm0YkNL5nxHag^_^server.ccl.net> X-Original-From: "Mi Yang" Date: Thu, 14 May 2009 06:24:07 -0400 Sent to CCL by: "Mi Yang" [shabbir3790()hotmail.com] Yes you are right! Besides dielectric constant it needs the density and radius at infinite frequency for the solvent of our own choice. How to achieve these parameters (Experimental or theoretical)for Dioxane still I am searching.Thankyou for your helpfull comments. Any addition would be appreciated Mi > "Alcides Simao alsimao^-^gmail.com" wrote: > > Sent to CCL by: Alcides Simao [alsimao:-:gmail.com] > --0015174bdfd8c7bdf20469db3d36 > Content-Type: text/plain; charset=ISO-8859-7 > Content-Transfer-Encoding: quoted-printable > > PCM methods are available in G03, if you read the manual carefully ( > http://www.gaussian.com/g_ur/k_scrf.htm ) > > However, as stated in the Gaussian manual: 'We list the =E5 values here for > convenience, but be aware it is only one of many internal parameters used t= > o > define solvents. Thus, simply changing the =E5 value will not define a new > solvent properly.' > > So, using CCl4 will not work (if it works, its plain coincidence, not > science!) > > In order to solve such problem, please read more about PCM methods in any > undergrad computational chemistry book and gather the data needed to solve > the problem! > > Best, > > Alcides > > --0015174bdfd8c7bdf20469db3d36 > Content-Type: text/html; charset=ISO-8859-7 > Content-Transfer-Encoding: quoted-printable > > PCM methods are available in G03, if you read the manual carefully ( f=3D"http://www.gaussian.com/g_ur/k_scrf.htm">http://www.gaussian.com/g_ur/= > k_scrf.htm )

However, as stated in the Gaussian manual: 'We= > =20 > list the =E5 values here for convenience, but be aware it is only one of=20 > many internal parameters used to define solvents. Thus, simply changing the= > =E5=20 > value will not define a new solvent properly.'

So, using CCl4 wi= > ll not work (if it works, its plain coincidence, not science!)

In or= > der to solve such problem, please read more about PCM methods in any underg= > rad computational chemistry book and gather the data needed to solve the pr= > oblem!
>
Best,

Alcides
> > --0015174bdfd8c7bdf20469db3d36-- > > From owner-chemistry@ccl.net Thu May 14 07:04:01 2009 From: "Marcel Swart marcel.swart||icrea.es" To: CCL Subject: CCL: Dioxane in PCM with G03 Message-Id: <-39322-090514064259-25508-symDzLKxK28Vc1o5rFyrgA.@.server.ccl.net> X-Original-From: Marcel Swart Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 14 May 2009 12:39:00 +0200 MIME-Version: 1.0 Sent to CCL by: Marcel Swart [marcel.swart=-=icrea.es] If you need the "molecular" radius, please have a look at: http://www.scm.com/Doc/Doc2008.01/ADF/ADFUsersGuide/page98.html#keyscheme%20= SOLVATION There is listed a number of solvents with "non-empirical" radii for use in dielectric continuum models; this set comes directly from principles set out in: M. Swart, E. R=F6sler and F.M. Bickelhaupt "Proton Affinities in Water of Maingroup-Element Hydrides. Effects of =20 Hydration and Methyl Substitution" Eur. J. Inorg. Chem. 2007, 3646-3654 If you need the macroscopic density of 1,4-dioxane, it is 1.0337 kg/l. Quoting "Mi Yang shabbir3790(a)hotmail.com" : > Yes you are right! Besides dielectric constant it needs the density =20 > and radius at infinite frequency for the solvent of our own choice. =20 > How to achieve these parameters (Experimental or theoretical) for =20 > Dioxane still I am searching. Thank you for your helpful comments. =20 > Any addition would be appreciated > > Mi =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.cat/Web/ScientificForm.aspx?key=3D372 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 From owner-chemistry@ccl.net Thu May 14 08:42:00 2009 From: "Andreas Klamt klamt\a/cosmologic.de" To: CCL Subject: CCL:G: Dioxane in PCM with G03 Message-Id: <-39323-090514084026-31014-ePFBa1PPFjdrDf5ZEy1/lA**server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 14 May 2009 14:40:11 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt++cosmologic.de] I partly disagree with this opinion of the others: If you just want to get the crude effect of the presence of a polarizable continuum of eps=2.22 around your solute, then for a polarizability calculation it should be by far good enough to use the settings of CCL4. All the other parameters may be needed in PCM in order to get a slightly better description of dG_solv but they should not matter significantly when calculating polarizabilities. Nevertheless, you need to be aware that it is just a dielectric continuum response. The much more important fact, that protic solutes will make hydrogen bonds with a dioxane solvent and thus have a different polarization than in a non-hydrogen-bond-accepting solvent, will not be included in a dielectric continuum calculation, whatever other parameters you choose. A way to take into account these non-dielectric effects would be Direct-COSMO-RS (see for example: Calculation of Solvent Shifts on Electronic g-Tensors with the Conductor-Like Screening Model (COSMO) and Its Self-Consistent Generalization to Real Solvents (Direct COSMO-RS) S Sinnecker, A Rajendran, A Klamt, M Diedenhofen, ... - J. Phys. Chem. A, 2006) which is in ORCA and TURBOMOLE. (In case you want to use it, please contact me before you start to use it. We have detected a small problem in Direct-COSMO-RS and you should use the updated code before using it.) Andreas Mi yang shabbir3790,+,hotmail.com schrieb: > Sent to CCL by: "Mi yang" [shabbir3790-#-hotmail.com] > Hello CCL user, > > Because my experiment data of polarizability is in Dioxane so I want to calculate polarizability in a Dioxane (Dielectric constant=2.22) with PCM method but this is not available in G03. > 1- Can I calculate polarizability by specifying the dielectric constant of 2.22 with read option in input or some other way to do this? > 2- If I choose a solvent (CCL4, dielectric constant= 2.228) which has dielectric constant near to Dioxane does it make sense? > > thanks > > Mi > > -- -------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt#cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------- From owner-chemistry@ccl.net Thu May 14 10:28:00 2009 From: "John McKelvey jmmckel^^gmail.com" To: CCL Subject: CCL: I7 vs PHENOM benchmarks Message-Id: <-39324-090514102603-2635-ZizFqZ3Ok+6bTy2GfJrhzQ _ server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=000e0cd2e590f14a8f0469e01aa9 Date: Thu, 14 May 2009 10:25:52 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel]_[gmail.com] --000e0cd2e590f14a8f0469e01aa9 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Are there any meaningful cpu intensive benchmarks [like quantum chem] available anywhere? Thanks! John McKelvey --000e0cd2e590f14a8f0469e01aa9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Are there any meaningful cpu intensive benchmarks [like quantum chem] available anywhere?

Thanks!

John McKelvey
--000e0cd2e590f14a8f0469e01aa9-- From owner-chemistry@ccl.net Thu May 14 12:53:00 2009 From: "Thomas Patko tpatko^^^gmail.com" To: CCL Subject: CCL: I7 vs PHENOM benchmarks Message-Id: <-39325-090514123121-3415-lNRRgAoSyrTgHw28gOE41w]*[server.ccl.net> X-Original-From: Thomas Patko Content-Type: multipart/alternative; boundary=0016364eed5865174b0469e0ddca Date: Thu, 14 May 2009 08:20:14 -0700 MIME-Version: 1.0 Sent to CCL by: Thomas Patko [tpatko\a/gmail.com] --0016364eed5865174b0469e0ddca Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello John: This is one such resource. It does include both Phenom and i7 benchmarks for a variety of QC job types (DFT, MP2, PM3,...). http://classic.chem.msu.su/gran/gamess/performance.html Cheers, Thomas On Thu, May 14, 2009 at 7:25 AM, John McKelvey jmmckel^^gmail.com < owner-chemistry-#-ccl.net> wrote: > Are there any meaningful cpu intensive benchmarks [like quantum chem] > available anywhere? > > Thanks! > > John McKelvey > --0016364eed5865174b0469e0ddca Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello John:

This is one such resource.=A0 It does include both Pheno= m and i7 benchmarks for a variety of QC job types (DFT, MP2, PM3,...).
<= br>http= ://classic.chem.msu.su/gran/gamess/performance.html

Cheers,

Thomas

On Thu, May 14,= 2009 at 7:25 AM, John McKelvey jmmckel^^gmail= .com <o= wner-chemistry-#-ccl.net> wrote:
Are there any mea= ningful cpu intensive benchmarks [like quantum chem] available anywhere?
Thanks!

John McKelvey

--0016364eed5865174b0469e0ddca-- From owner-chemistry@ccl.net Thu May 14 13:27:01 2009 From: "Joy Ku joyku|-|stanford.edu" To: CCL Subject: CCL: Molecular Dynamics Workshop Series Message-Id: <-39326-090514124710-4749-bH8HZ1RoIm8ada2m5WEuvA\a/server.ccl.net> X-Original-From: "Joy Ku" Date: Thu, 14 May 2009 12:47:06 -0400 Sent to CCL by: "Joy Ku" [joyku::stanford.edu] When: * OpenMM Developers Workshop for speeding up your molecular dynamics code on GPUs June 24, 2009 (additional days for integration of OpenMM June 25-26, 2009) * Introduction to Markov State Models and MSMBuilder for analyzing molecular dynamics results June 25, 2009 * Introduction to Molecular Dynamics & OpenMM Zephyr June 26, 2009 Where: Stanford University === Details === The free upcoming Molecular Dynamics Workshop Series sponsored by Simbios, an NIH National Center for Biomedical Computing, consists of three workshops, showcasing software designed for individuals with different interests and experience with MD, from novices to experts. The OpenMM Developers Workshop is geared towards developers who are interested in using the OpenMM library to enable their MD code to run on high performance computer architectures. The current version of the freely downloadable OpenMM enables MD codes to run on NVIDIA and ATI GPUs and has shown 100X.* The workshop will highlight the explicit solvent capabilities that will be available in the next OpenMM release in June and include a special track focused on integration of OpenMM into AMBER. Introduction to Molecular Dynamics and OpenMM Zephyr is for researchers interested in using MD in their research, including novices to MD. You will learn the theory behind MD and use the OpenMM Zephyr application, which makes it easy to run and visualize MD simulations. OpenMM Zephyr incorporates the OpenMM library, enabling acceleration of the simulations on GPUs. Introduction to Markov State Models and MSMBuilder is for researchers who want to analyze the results of MD simulations, mapping out the metastable states of a molecule and the transition rates between them. You will learn about Markov State Models and why they are suitable for this, and use the MSMBuilder software to automatically construct such models, as well as analyze and visualize them. Registration is free but required and spaces are limited. For more details, visit http://simbios.stanford.edu/MDWorkshops.htm -------------------------------------------------------------------------- OpenMM, OpenMM Zephyr, and MSMBuilder are supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures, as part of its protein folding research efforts. To learn more about Simbios and its research and software tools, visit http://simbios.stanford.edu. *OpenMM accelerated code running on Nvidia GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6), 864-872. From owner-chemistry@ccl.net Thu May 14 17:19:00 2009 From: "Madi madi7sk%a%gmail.com" To: CCL Subject: CCL:G: Dioxane in PCM with G03 Message-Id: <-39327-090514171741-25997-PQGpG1Rv7ihgw84RWXtJxA(a)server.ccl.net> X-Original-From: Madi Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Date: Thu, 14 May 2009 17:17:29 -0400 MIME-Version: 1.0 Sent to CCL by: Madi [madi7sk{:}gmail.com] Hi, I was trying to specify DMF using the PCM model in gaussian and was having trouble getting it to work. I wrote to gaussian and their reply was very helpful. I am attaching it here for your reference. After you are done specifying all the parameters, make sure you deliberately leave a blank line. Hope this helps madi ****************************************************************** Regarding the specification of the DMF solvent, even though only the solvents listed in the Gaussian documentation of the SCRF keyword are available through the "Solvent=3D" option, a different solvent may be explicitly defined in the PCM input. However, please, note that it is not possible to input all parameters that define an arbitrary solvent. Specifically, one cannot define all of the terms necessary to calculate the non-electrostatic contributions. For this reason, there are two recommended alternatives: 1) Check in the list of solvents provided for the SCRF keyword whether there is a solvent similar enough to the one you would like to use in your calculation and provide this name in the "Solvent" option of the SCRF keyword. Then, add also the "Read" option to provide the modifications of "EPS", "RSOLV", "Density", and "VMOL". This way, you would be introducing the parameters for your desired solvent, for the cases of parameters that are available for user input, and the program would be using the closest possible parameters for those other parameters that are not available for user input. (Note: if no solvent is specified, then the program defaults to water). So, probably, your best choice here would be to select a solvent with similar properties to DMF (such as Acetonitrile, DMSO, Acetone, Nitromethane) and then give the corresponding "EPS", "RSOLV", "Density", and "VMOL" parameters for DMF. 2) Alternatively, you can use the options "NoDis NoRep NoCav" in order to prevent the use of the parameters for the internally stored solvent (water, by default), so the non-electrostatic contributions to the solvation energy will not be computed. Note also that this is true if the default "UA0" radii are used, the electrostatic terms are then correctly computed this way. If this is not the case, and the UAHF or UAKS radii are used, then there is a dependency of the radius with the type of solvent so it would not be correct to use a modified water as a model for a solvent with properties different than water. Thus, if UAHF or UAKS radii are used, then one has to still do what it was explained in the previous paragraph, 1), (that is to use the "Solvent=3D" option to select, from the list of predefined solvents, a solvent similar to the one you are interested in). For the calculation of only the electrostatic part, you can define the solvent by defining the dielectric constant using the "EPS" option, the solvent radius using the "RSOLV" option, and the dielectric constant at infinite frequency using the "EPSINF". EPSINF is the dielectric constant at infinite frequency. It is an experimentally measured value. The value of EPSINF will not affect the results of ground-state energy calculation of DeltaG(solv), so you do not need to worry about getting a non-standard value. EPSINF is only necessary when performing excited state PCM calculations. Other than EPS, RSOLV usually makes the biggest difference in the result. As for choosing a value of RSOLV, our developers recommended a couple of references they use for this parameter: * O. Sinanoglu in "Molecular Interactions" Z. Ratajczack and Orville-Thomas eds, Wiley 1982 vol. 3 chap. 6 * M.H. Abraham and A. Nasehzadeh J. Chem. Soc. Faraday Trans. 1 1981, 77, 3= 40. If the desired RSOLV parameter is not found there, the molar volume may give some hints for RSOLV values for new solvents, even though attention must be paid to the chemical nature of the solvent, because strong interactions modify, to some extent, the definition of the hard sphere analogue of the solvent molecular volume. Thus, although a simple approximation, the Stearn-Eyring formula (Stearn, Eyring J. Chem. Phys. 1937, 5, 113) can be used to derive a value for RSOLV, given the molar volume of the solvent. Finally, about other parameters, which only affect the non-electrostatic terms, the DENSITY is a "number density", i.e. number of particles per volume, and the units are Angstroms^=963. Taking the density of the solvent in "g * cm^=963", divide by the molar weight of the solvent and multiply by Avogadro's number to transform the grams into number of particles, and, finally, divide by 10^24 to transform cm^=963 into Angstrom^=963. Although the density and the molar volume are obviously related, these two quantities are used by the program to compute two different energy contributions and, unfortunately, they were introduced in the code as two independent parameters. Thus, the user needs to provide both the density ("DENSITY" PCM keyword) and the molar volume ("VMOL" PCM keyword) in order to set the desired modifications, so the two of them are consistent with each other. The units of the density are Angstrom^=963 while the units of the molar volume are cm^3. So, from the value of the density of the solvent in "g * cm^=963", take the inverse of the density and then divide by the molar weight of the solvent in order to get the molar volume in cm^3. Enter this parameter in your input file with the "VMOL" PCM keyword. The following input will use the standard parameters for the solvent given in "Solvent=3D", and modify those given in the additional PCM options (the values given below are not representative of any particular solvent and they are only given as an example of how to use these keywords): % #P SCRF=3D(PCM,Solvent=3D,READ) / <Charge Multiplicity> <Coordinates> EPS=3D6.0 RSOLV=3D1.6 DENSITY=3D0.045 VMOL=3D19.05