From owner-chemistry@ccl.net Thu Oct 16 02:00:00 2008 From: "Sengen Sun sengensun[]yahoo.com" To: CCL Subject: CCL: Quantitative empirical rules, not really theories. Message-Id: <-37922-081016015820-25884-bnBpSQAMm6G0KeDIeSZD9Q=server.ccl.net> X-Original-From: Sengen Sun Content-Type: text/plain; charset=us-ascii Date: Wed, 15 Oct 2008 22:58:08 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun(a)yahoo.com] The three big things in theoretical org chem: W-H rules, FMO theory, and conceptual DFT, have a common problem. There are experimental facts against what they say. > According to Popper's reasoning, they are not scientific theories. Kuhn disagreed with Popper. Kuhn argued that people in the main stream community do not accept Popper's reasoning. Instead, they would try hard to repair, to find excuses for, to decorate, and to cover up the flaws, and to resist a new theoretical revolution by a single person or a few. I like these 2 big philosophers. These 2 big names have special philosophical meanings. If their names are misused, philosophy of science may be turned upside down. > An argument for conceptual DFT from one of the private e-mails is "nothing is perfect, as no body is". But a half of century ago, we knew that many strange reactions cannot be understood based on the electrophilicity and nucleophilicity, which induced decades-long and heated debate about the reasons for these strange reactions. The conceptual DFT was bound to fail at the first place before it was started. > For the last half century, the major effort in theoretical org chem has been focused on quantifying empirical knowledge or empirical rules, chasing behind experimental results. As mentioned in my archived slides, what we really got are the quantitative empirical rules, not truly theories. This is the essence of the three big things, which fail any time as an empirical rule does. Are they all that the powerful computational chemistry can offer for chemical reactions? > Human can now design many things computationally such as spaceships. If theoreticians wish to master chemical reactions computationally in the coming centuries, it is unavoidable that physical behaviors of electron density between and around nuclei be thoroughly understood and computationally manipulated. > Thanks to every one for your patience. I am sorry for posting too many. > Sengen From owner-chemistry@ccl.net Thu Oct 16 06:25:01 2008 From: "mahmoud khedr mkkhedr#hotmail.com" To: CCL Subject: CCL: Molecular Dynamics Message-Id: <-37923-081016062054-2105-RD5JXO9xnDYN4dYN5zeKIw+*+server.ccl.net> X-Original-From: mahmoud khedr Content-Type: multipart/alternative; boundary="_c2f6c5a2-8fd1-4c04-a0df-b180b7594320_" Date: Thu, 16 Oct 2008 09:50:43 +0000 MIME-Version: 1.0 Sent to CCL by: mahmoud khedr [mkkhedr(!)hotmail.com] --_c2f6c5a2-8fd1-4c04-a0df-b180b7594320_ Content-Type: text/plain; charset="windows-1256" Content-Transfer-Encoding: 8bit Dear All, Thanks a lot for you. Regards, Mahmoud > From: owner-chemistry[#]ccl.net > To: mkkhedr[#]hotmail.com > Subject: CCL: Molecular Dynamics > Date: Tue, 14 Oct 2008 10:36:31 +0100 > > > Sent to CCL by: Chris Howard [c.k.howard(a)reading.ac.uk] > > Wikipedia has a very good overview of Molecular Dynamics: > > http://en.wikipedia.org/wiki/Molecular_dynamics > > Modelling crystals can be done with molecular Dynamics but be aware of the > limitation on cell size (i.e., dont expect good simulations on desktop pcs > above ~3000 Atoms). > > > A good piece of software for Molecular Dynamics is DL_POLY_2: > > http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/ > > I have used it to model both crystals and amorphous materials. > > > Some general tips for Molecular Dynamics: > > - Your results will only be as good as the Potential you use and its > parameters - A linear increase in the number of atoms tends to increase > simulation time exponentially - Give alot of thought to boundary > conditions!! > > I hope that's a good starting point. > > Chris > > On Oct 14 2008, Mahmoud Korani Abdel-Latif mkkhedr**hotmail.com wrote: > > > > >Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr a hotmail.com] > >Dear CCLers, > >First, thanks in advance > > > > Second, I would like to do molecular simulation for some bio crystals > > using CPMD program but unfortunately, it is the first time to me to make > > molecular dynamics. So I need some simple available references to learn > > about MD. Is it available to do molecular dynamics for crystals or not? > > > >What should I start with? > >Thanks again. > > > >Best Regards> > _________________________________________________________________ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE --_c2f6c5a2-8fd1-4c04-a0df-b180b7594320_ Content-Type: text/html; charset="windows-1256" Content-Transfer-Encoding: 8bit Dear All,

Thanks a lot for you.

Regards,
Mahmoud

> From: owner-chemistry[#]ccl.net
> To: mkkhedr[#]hotmail.com
> Subject: CCL: Molecular Dynamics
> Date: Tue, 14 Oct 2008 10:36:31 +0100
>
>
> Sent to CCL by: Chris Howard [c.k.howard(a)reading.ac.uk]
>
> Wikipedia has a very good overview of Molecular Dynamics:
>
> http://en.wikipedia.org/wiki/Molecular_dynamics
>
> Modelling crystals can be done with molecular Dynamics but be aware of the
> limitation on cell size (i.e., dont expect good simulations on desktop pcs
> above ~3000 Atoms).
>
>
> A good piece of software for Molecular Dynamics is DL_POLY_2:
>
> http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/
>
> I have used it to model both crystals and amorphous materials.
>
>
> Some general tips for Molecular Dynamics:
>
> - Your results will only be as good as the Potential you use and its
> parameters - A linear increase in the number of atoms tends to increase
> simulation time exponentially - Give alot of thought to boundary
> conditions!!
>
> I hope that's a good starting point.
>
> Chris
>
> On Oct 14 2008, Mahmoud Korani Abdel-Latif mkkhedr**hotmail.com wrote:
>
> >
> >Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr a hotmail.com]
> >Dear CCLers,
> >First, thanks in advance
> >
> > Second, I would like to do molecular simulation for some bio crystals
> > using CPMD program but unfortunately, it is the first time to me to make
> > molecular dynamics. So I need some simple available references to learn
> > about MD. Is it available to do molecular dynamics for crystals or not?
> >
> >What should I start with?
> >Thanks again.
> >
> >Best Regards>
> >
> ; >
>
>
>
>
>
>
>
>
>
>
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>
>
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>
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Explore the seven wonders of the world Learn more! --_c2f6c5a2-8fd1-4c04-a0df-b180b7594320_-- From owner-chemistry@ccl.net Thu Oct 16 08:44:00 2008 From: "Szori_Milan milan##jgypk.u-szeged.hu" To: CCL Subject: CCL:G: Gaussian Thermochemistry Message-Id: <-37924-081016062411-2310-7jq+J5JjBhj9qQY+IcucEw . server.ccl.net> X-Original-From: Szori_Milan Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-2 Date: Thu, 16 Oct 2008 11:51:57 +0200 MIME-Version: 1.0 Sent to CCL by: Szori_Milan [milan^-^jgypk.u-szeged.hu] Hi Lynn

The first problem is the dimension of entropy ...=A0 that should be calmol-1K-1. That=A0 is exactly what you can find in th= e output (this is an example in case of F2 calculated at HF/6-31G* level of= theory [# HF/6-31G* Opt Freq].):
=A0
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 E (Therm= al)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 CV=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0 S
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 KCal/= Mol=A0=A0=A0=A0=A0=A0=A0 Cal/Mol-Kelvin=A0=A0=A0 Cal/Mol-Kelvin
=A0Total=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 3.2= 70=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 5.145=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 48.115
=A0Electronic=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.000=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.000=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0 0.000
=A0Translational=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.889=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0 2.981=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 36.834
=A0Rotational=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.592=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1.987=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= 11.247
=A0Vibrational=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1.789=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.177=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= 0.034

Best,
Milan Szori=20
=20
Department of Chemical Informatics=20
Faculty of Education, University of Szeged=20



On Mon, 13 Oct 2008 19:03:56 -0400, Shina Lynn Ka= merlin skamerli]*[usc.edu=20 wrote
>=20 Sent to CCL by: "Shina Lynn Kamerlin" [skamerli]=3D[usc.edu]=20
>=20 Dear all,=20
>=20
>=20 I have a quick query regarding gaussian thermochemistry output. I am trying= to=20 look at gas phase entropies, particularly the entropy decomposition (i.e.= =20 translational, rotational, vibrational) from standard gaussian thermochemis= try=20 calculations. I am looking at large-ish systems, and the numbers I got seem= ed=20 very strange, so I decided to try something very simple, just dimerisation = of F2=20 to see if what I am doing is working. For dimerisation, I think I would exp= ect=20 ~10kcal/mol, except, what I get is quite strange:=20
>=20
>=20 Entropy =A0 =A0 =A0 =A0 =A0 F2 =A0 =A0 =A0 =A0 =A0=20 F=20
>=20 Translational =A0 =A010.8 =A0 =A0 =A0 =A010.4=20
>=20 Rotational =A0 =A0 =A0 =A03.4 =A0 =A0 =A0 =A0 0.0=20
>=20 Vibrational =A0 =A0 =A00.04 =A0 =A0 =A0 =A0 0.0=20
>=20 Total =A0 =A0 =A0 =A0 =A0 =A014.2 =A0 =A0 =A0 =A0 10.4=20
>=20
>=20 (these are in kcal/mol, assuming 298K, taken from the cal/mol-kelvin value = given=20 in the gaussian output).=20
>=20
>=20 I am clearly doing something wrong, I just have no idea what. Any=20 advice/suggestions would be hugely appreciated!=20
>=20
>=20 Thanks,=20
>=20
>=20 Lynn=20
>=20
>=20 -=3D This is automatically added to each message by the mailing script =3D-= =20
>=20=20
>=20=20
>=20=20
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>=20 Subscribe/Unsubscribe:=20=20
>=20 =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml=20
>=20
>=20 Before posting, check wait time at: http://www.ccl.net=20
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>=20 Job: http://www.ccl.n= et/jobs=20=20
>=20 Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/=20
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>=20 Search Messages: htt= p://www.ccl.net/htdig =A0(login: ccl, Password:=20 search)=20
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>=20 =A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt=20
>=20
>=20 RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/=20



From owner-chemistry@ccl.net Thu Oct 16 09:52:01 2008 From: "Russell D Johnson III russell.johnson _ nist.gov" To: CCL Subject: CCL:G: Small molecules with HF SCF convergence difficulty Message-Id: <-37925-081015154107-20425-6b+P/mbCMAU+jTA7HBNePg|,|server.ccl.net> X-Original-From: Russell D Johnson III Content-Type: text/plain; charset="us-ascii" Date: Wed, 15 Oct 2008 14:59:02 -0400 Mime-Version: 1.0 Sent to CCL by: Russell D Johnson III [russell.johnson_-_nist.gov] Hello Adam, In running calculations for the Computational Chemistry Comparison and Benchmark Database (http://cccbdb.nist.gov) I have run into SCF convergence problems, but, unfortunately, until recently have not been systematically keeping track of failures. I do have some examples where, when using the Gaussian package, I used scf=qc in the route section. The following molecules needed this option with the HF/6-31G* model chemistry: CH3COOH CH3O CH3S CP CuO FOO NO NS O C6H5 (phenyl radical) PO For the HF/6-31+G** model chemistry there is also: Cl CH3CH2O At 07:10 PM 10/13/2008, you wrote: >Sent to CCL by: Adam Hunter [spacyhunter#gmail.com] >hi, all, > I'm studying the SCF convergence problem. Can anybody provide me some small molecules which are hard to converge with the Hartree-Fock method? I know several such examples with DFT convergence difficulty, but have not found good examples for the Hartree-Fock method. > Any help will be greatly appreciated. Thank you very much! >all the best >Adam Dr. Russell D. Johnson III Research Chemist National Institute of Standards and Technology Computational Chemistry Group 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301+975-2513 fax:301+869-4020 email: russell.johnson{}nist.gov From owner-chemistry@ccl.net Thu Oct 16 10:59:01 2008 From: "Peter Ryan ryanp- -tcd.ie" To: CCL Subject: CCL: augmented charge density in Ultra Soft Pseodopotentials .. can someone explain ? Message-Id: <-37926-081016105629-8716-QlbAE0VdIWvL1uzbkJXZog-*-server.ccl.net> X-Original-From: "Peter Ryan" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 16 Oct 2008 15:56:18 +0100 MIME-Version: 1.0 Sent to CCL by: "Peter Ryan" [ryanp|-|tcd.ie] Hi Folks. In reading up on the details of ulta soft pseudopotentials i have come acros this sentance and varients of it quite a lot. .....In order to recover the full electronic charge of the system when using ultra soft pseudo potentials , the electron density given by the square moduli of the wavefunctions is augmented in the core regions. ... Can someone please explain what the phrase "augmented" actually means in this context. Are we just adding back the charge that we have just removed while implementing ultra soft pseudopotentials ? i don't get it : ) Whats the point if the charge is just added back ... regards peter. From owner-chemistry@ccl.net Thu Oct 16 11:54:01 2008 From: "Dennis Devine sahaimic(!)gmail.com" To: CCL Subject: CCL:G: Counterpoise Calculations in G03 Message-Id: <-37927-081016113915-28299-kJWn53U4EtQKeaOM5hrX0A[]server.ccl.net> X-Original-From: "Dennis Devine" Date: Thu, 16 Oct 2008 11:39:11 -0400 Sent to CCL by: "Dennis Devine" [sahaimic * gmail.com] Hi I want to do calculations on a system composed of selected receptor residues and the ligand using the Gaussian program to obtain interaction energies for each of the fragments of the system. In the end i hope to understand which fragment contributes most to the stability of the system. But i am not sure how to go about this. I am trying to do it by first using an energy minimized structure of the full protein obtained from MD simulations on GROMACS. Then selecting key residues and the ligand and then doing the energy calculations using Gaussian. But i am sure this is not enough and i need to compensate for BSSE using the CP method. However, i am not sure how these files can be set up. Ideally I want to use the locally dense basis set (LDBS) approach, where the model-system will been partitioned into two different regions, which were assigned basis sets of different accuracy. The atoms interacting directly with the ligand and the ligand itself will be described by 6-31g* basis set. While the less accurate 3-21G* basis set will be used for all remaining atoms. I plan on using the MP2 level of theory. Say i am looking at the interaction energy of one residue and the ligand. Do i need to set up 3 files to calculate the interaction energy using G03. Namely: 1. With the counterpoise=2 in the route card with the fragments described - with the mixed basis set. 2. Fragment one - energy calculation with its basis set. 3. Fragment two - energy calculating with its basis set. and the calculation in the end would be E(int)CP = System (CP) - (F1+F2) (all in hartrees - then converted to KJ/mol) Any comments and suggestions in how to go about doing this would be most appreciated. Thank you very much in advance for the assistance. Best regards, Dennis sahaimic---gmail.com From owner-chemistry@ccl.net Thu Oct 16 12:32:01 2008 From: "Roman D. Gorbunov rgorbuno+/-aecom.yu.edu" To: CCL Subject: CCL:G: Overtone anharmonicities and anharmonic frequencies from Gaussian. Message-Id: <-37928-081016122604-20170-+kLRHPYrfJDI8PzOibj/hg]_[server.ccl.net> X-Original-From: "Roman D. Gorbunov" Date: Thu, 16 Oct 2008 12:26:00 -0400 Sent to CCL by: "Roman D. Gorbunov" [rgorbuno _ aecom.yu.edu] Dear CCL subscribers, I need to calculate overtone anharmonicities of vibrational modes of a molecule. In other words I need to know (E_1 - E_0) - (E2 - E1), where E_j are energy levels of a vibrational states. I have managed to get a normally terminated Gaussian calculations of anharmonic frequencies (using Freq=(HPModes,Anharmonic)). So, in my output file I have harmonic and anharmonic frequencies of the normal modes. The problem is that I do not know how the "overtone anharmonicities" are related with the "anharmonic frequencies". The problem is that I do not know the definition for the anharmonic frequencies. I can try to ges. May be "anharmonic frequency" are defined as the transition frequency from the first excited state to the ground state in the cubic potential? But even if it is defined like that it still does not give a direct answer on my question (how to get the overtone anharmonicites). Can anybody help me with that? Thank you in advance. From owner-chemistry@ccl.net Thu Oct 16 17:07:01 2008 From: "N. Sukumar nagams|a|rpi.edu" To: CCL Subject: CCL: augmented charge density in Ultra Soft Pseodopotentials .. can someone explain ? Message-Id: <-37929-081016164015-30467-CY6X8L4EcoMnGygbiZscLg{:}server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Thu, 16 Oct 2008 16:39:15 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams/a\rpi.edu] While I'm not familiar with the details of ultra soft pseudopotentials, the point of using pseudopotentials on heavy atoms is that you avoid the need for basis functions for the (generally unimportant) core electrons (and the associated integral calculations), thereby reducing the dimensions of the equations to be solved (matrices to be diagonalized) and saving drastically on computing time. But of course, since you don't have core electrons now, the electron density will not be correct in the core regions; hence the need for the correction. N. Sukumar Associate Research Professor of Chemistry and Chemical Biology Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute http://reccr.chem.rpi.edu/ ==============Original message text=============== On Thu, 16 Oct 2008 10:56:18 EDT "Peter Ryan ryanp- -tcd.ie" wrote: Sent to CCL by: "Peter Ryan" [ryanp|-|tcd.ie] Hi Folks. In reading up on the details of ulta soft pseudopotentials i have come acros this sentance and varients of it quite a lot. .....In order to recover the full electronic charge of the system when using ultra soft pseudo potentials , the electron density given by the square moduli of the wavefunctions is augmented in the core regions. ... Can someone please explain what the phrase "augmented" actually means in this context. Are we just adding back the charge that we have just removed while implementing ultra soft pseudopotentials ? i don't get it : ) Whats the point if the charge is just added back ... regards peter.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Thu Oct 16 17:56:00 2008 From: "David A. Case case(0)biomaps.rutgers.edu" To: CCL Subject: CCL: Disgeo and/or DGII source Message-Id: <-37930-081016072902-11330-d98M/p0pquyq0WUkaSNeeA[-]server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 16 Oct 2008 07:28:44 -0400 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case]~[biomaps.rutgers.edu] On Wed, Oct 15, 2008, Mark Umbarger umbarger,+,fas.harvard.edu wrote: > > Sent to CCL by: "Mark Umbarger" [umbarger#fas.harvard.edu] > > I am wondering if anyone could point me to source code for the disgeo > or dgII distance geometry implementations. I have implemented a new > experimental technique to measure the distances between loci on bacterial > chromosomes and would like to use distance geometry to generate an ensemble > of structures from these distances. These are pretty old programs. A version of DGEOM95 is described here: http://www.ccl.net/chemistry/resources/messages/1995/03/09.008-dir/index.html But it might be easier to work with the distance geometry capability in programs like Tinker or NAB or X-PLOR-NIH: http://dasher.wustl.edu/tinker/ http://ambermd.org/#AmberTools http://nmr.cit.nih.gov/xplor-nih/ Any one of these should help you create a program that does the sort of thing you describe. And I'm sure there are other distance geometry codes out there; others on the list can chime in with their own experience -- mine is mostly with NAB. ...dave case From owner-chemistry@ccl.net Thu Oct 16 21:17:01 2008 From: "willsd^^^appstate.edu" To: CCL Subject: CCL:G: Overtone anharmonicities and anharmonic frequencies from Gaussian. Message-Id: <-37931-081016182001-7602-fh1ZCi+j4gZsvO4qTr/p7w%a%server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 16 Oct 2008 21:38:29 GMT MIME-Version: 1.0 Sent to CCL by: [willsd*appstate.edu] 'd recommend the VSCF method in GAMESS. You can specify how many quanta you want. So in a three mode system (like water, perhaps) with vibrational quantum numbers (n1, n2, n3) you can compute the vibrational energies of a variety of excitations: fundamentals:(1,0,0); (0,1,0); (0,0,1) first overtones: (2,0,0); (0,2,0); (0,0,2) second overtones: (3,0,0), (0,3,0), (0,0,3) (Differences between these and 2x or 3x the fundamentals will give you the first and second anharmonicities) combination bands: (1,1,0); (1,0,1), (0,1,1) higher combinations: (2,1,0), (1,2,0), (2,0,1), (1,0,2), (0,1,2), (0,2,1) It is possible to compute the potential with all combinations of three (not just one or two) modes, but I am not sure if you can get energies with excitations in three different modes. GAMESS can also compute dipoles at all points on the one (or one and two) mode grids it uses, so it can also estimate IR intensity for these excitations, not just the frequencies. There are a LOT of grid points for two mode calculations even for smallish (say 10 atom) molecules, and rather good energies are needed to get good frequencies, so it can be slow... a triple zeta mp2 calculation for C4H5N may take several weeks on 8 cores of a xeon based cluster. The results are really quite good though... many fundamentals, overtones, and combination bands predicted within 20 cm-1 or so of observed frequencies, with relative intensities close enough to observed intensities to be useful for assigning spectra. Steve Williams ----- Original Message ----- > From: "Roman D. Gorbunov rgorbuno+/-aecom.yu.edu" Date: Thursday, October 16, 2008 1:18 pm Subject: CCL:G: Overtone anharmonicities and anharmonic frequencies from Gaussian. To: "Williams, Steve " > > Sent to CCL by: "Roman D. Gorbunov" [rgorbuno _ aecom.yu.edu] > Dear CCL subscribers, > > I need to calculate overtone anharmonicities of vibrational modes > of a molecule. In other words I need to know (E_1 - E_0) - (E2 - > E1), where E_j are energy levels of a vibrational states. > > I have managed to get a normally terminated Gaussian calculations > of anharmonic frequencies (using Freq=(HPModes,Anharmonic)). So, in > my output file I have harmonic and anharmonic frequencies of the > normal modes. > > The problem is that I do not know how the "overtone > anharmonicities" are related with the "anharmonic frequencies". The > problem is that I do not know the definition for the anharmonic > frequencies. I can try to ges. May be "anharmonic frequency" are > defined as the transition frequency from the first excited state to > the ground state in the cubic potential? But even if it is defined > like that it still does not give a direct answer on my question > (how to get the overtone anharmonicites). > > Can anybody help me with that? > > Thank you in advance. > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the ~ sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > >