From chemistry-request@server.ccl.net Tue Aug 28 02:36:28 2001 Received: from gamma.dou.dk (frj@[130.225.156.12]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7S6aRM29296 for ; Tue, 28 Aug 2001 02:36:27 -0400 Received: from localhost (frj@localhost) by gamma.dou.dk (8.9.3/8.9.3) with ESMTP id IAA28370; Tue, 28 Aug 2001 08:36:23 +0200 (METDST) Date: Tue, 28 Aug 2001 08:36:22 +0200 (METDST) From: Frank Jensen To: elewars cc: chemistry@ccl.net Subject: Re: CCL:combination of b3lyp and cc-pVQZ In-Reply-To: <3B8A6D2C.66544C09@trentu.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII We have recently done some benchmarking of various basis set for DFT. For the H,C,N,O,F molecules in the G3 data set, the MAD and Maximum error of some popular basis sets for total atomization energies with the BLYP functional are (kJ/mol): MAD Max 6-31G* 16 64 cc-pVDZ 41 82 cc-pVTZ 3.6 14.5 cc-pVQZ 2.9 10.9 These numbers are errors relative to a saturated basis set, i.e. the Kohn-Sham limit. The values should be fairly independent on the functional, including hybrid functionals like B3LYP. The basis set error should of course be compared to a typical error inherently in the functional itself, which for e.g. B3LYP may be ~20 kJ/mol. For relative energies between similar species the basis set error is likely to be smaller, but we have no hard data on this yet. Frank On Mon, 27 Aug 2001, elewars wrote: > > Hello, > > DFT calc's seem to be "saturated" by basis sets more quickly than are ab initio: > Merril et al noted that "Once the double split-valence level [e.g. 6-31G*] is > reached, further improvement in basis set quality offers little in the way of > structural or energetic improvement.' [1]. Stephens et al. report that "B3LYP > calculations converge rapidly with increasing basis set size and that the > cost-to-benefit ratio is optimal at the 6-31G* basis set level. 6-31G* will be > the basis set of choice in B3LYP calculations on much larger molecules [than > C5H6O2]." [2]. We have found (albeit in a limited number of calculations) only > very small differences (up to 4 kJ mol-1) between 6-31G* and 6-311G* basis sets > with the BP86 functional. > > But you could do some test calculations using B3LYP/6-31G* and B3LYP/cc-pVQZ. > > [1] G. N. Merrill, S. Gronert, S. R. Kass, J Phys Chem A, 1997, 101, 208. > [2] P. J. Stephens, F. J. Devlin, C. F. Chablowski, M. J. Frisch, J Phys Chem > 1994, 98, 11623, and refs therein. > > E. Lewars > ========= > > > Harald Bock wrote: > > > Dear reader, > > I have a question about combining methods and basis sets: > > > > does it make sense to run a calculation usin eg b3lyp using a cc-pVQZ > > basis set. I am interested in opt, freq (raman) and nbo results. > > > > Harald Born > > > > Please send answers to > > > > protactinium@gmx.de > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > -------------------------------------------------- | Frank Jensen, Department of Chemistry | | SDU Odense University, DK-5230 Odense, Denmark | | FAX +45 66 15 87 80 , Voice +45 65 50 25 07 | | http://www.sdu.dk/Nat/Chem/STAFF/sci/FrjE.html | | http://bogense.chem.ou.dk/~frj | -------------------------------------------------- From chemistry-request@server.ccl.net Tue Aug 28 06:09:30 2001 Received: from c0mailgw13.prontomail.com ([216.163.180.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7SA9QM19415 for ; Tue, 28 Aug 2001 06:09:29 -0400 Received: from c0web110 (216.163.180.10) by c0mailgw13.prontomail.com (NPlex 5.5.029) id 3B7C46F70029AEF2 for chemistry@ccl.net; Tue, 28 Aug 2001 03:02:06 -0700 From: "markus mayer" Message-Id: <7C03650B99B95D115A6600807CFBC69C@mayer.nandomail.com> Date: Tue, 28 Aug 2001 03:02:06 -0800 X-Priority: Normal Content-Type: text/plain; charset=ISO-8859-1 To: chemistry@ccl.net Subject: empirical potential for C and H X-Mailer: Web Based Pronto Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Dear all, does anybody know some simple potential (preferably that fitted to experiments) which describe the interaction between Hydrogen and sp, sp2 and sp3 carbon? I wish to have the non-bonded interaction. thanks in advance markus ________________________________________________________________ To get your free Web-based E-mail go to http://www.nandomail.com From chemistry-request@server.ccl.net Tue Aug 28 08:44:17 2001 Received: from janus.hosting4u.net ([209.15.2.37]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7SCiHM24842 for ; Tue, 28 Aug 2001 08:44:17 -0400 Received: (qmail 17449 invoked from network); 28 Aug 2001 12:44:17 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 28 Aug 2001 12:44:17 -0000 Received: from yersina ([202.138.16.231]) by proinformatix.com ; Tue, 28 Aug 2001 07:44:13 -0500 Reply-To: From: "Sergio Manzetti" To: "Bernd Rupp" Cc: "Chemistry Discussion G" Subject: RE: CCL:GROMACS and Energy Minimization Date: Tue, 28 Aug 2001 22:42:44 -0700 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal In-Reply-To: <10108281134.ZM157021@alberich05.pharm.uni-duesseldorf.de> Hi and thanks for all help. I am though very curious about one thing in GROMACS. When simulationg dimers in water, in the cases with inhibitors/substrates the non-covalent binding forces between the two chains might not be favourable. In this case, the reasonable result would be a slight (or strong) dissociation in vitro. The constraint parameters in the parameter file in GROMACS make this dissosiation impossible as far as I have understood, and the mdrun script, when runned constraints will not allow such dissociation (I presume). In this case, the energy will be the only reliable factor to deduce something about a enzyme and substrate complex. If I add constraint parameters in the *mdp file, the chains will probably be held together anyway, but the mdrun stops because of unusual bond lengths and violated constratints. What I would like to know, is HOW should I set the parameters to make this dissociation possible (if possible in GROMACS?), and finalize the molecular simulation with graphical and visual data. Thank you all Sergio ____________________________________________________________________________ ___________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ -----Original Message----- From: Bernd Rupp [mailto:rupp@pharm.uni-duesseldorf.de] Sent: Tuesday, August 28, 2001 2:34 AM To: Sergio Manzetti Subject: Re: CCL:GROMACS and Energy Minimization Hi Sergio, here is an example file, with wich i have calculated insulin dimers(also more chains). hopefully it runs also on you machine. if you have more questions, you can ask me; but i am also only an user.!? ;-)) what GROMACS version runs on you machine and wich kind of machines do you have. chiao Bernd -- Bernd Rupp Heinrich-Heine-Universitaet Duesseldorf | Gebaeude 26.23 Raum O2.33 Institut fuer Pharmazeutische Chemie | Tel.: 0211 / 81 - 1 38 27 Universitaetsstr. 1 | Fax.: 0211 / 81 - 1 38 47 40225 Duesseldorf | E-Mail: rupp@pharm.uni-duesseldorf.de From chemistry-request@server.ccl.net Tue Aug 28 08:51:09 2001 Received: from janus.hosting4u.net ([209.15.2.37]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7SCp8M24985 for ; Tue, 28 Aug 2001 08:51:08 -0400 Received: (qmail 19732 invoked from network); 28 Aug 2001 12:51:09 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 28 Aug 2001 12:51:09 -0000 Received: from yersina ([202.138.16.231]) by proinformatix.com ; Tue, 28 Aug 2001 07:51:03 -0500 Reply-To: From: "Sergio Manzetti" To: "Chemistry Discussion G" Subject: GROMACS simulation trajectories Date: Tue, 28 Aug 2001 22:49:36 -0700 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal Hi all, I would like to know if anyone knows about any programs that can work with the trajectories outputted from GROMACS, and visualize and maybe even export them to AVS file formats. Cheers Sergio ____________________________________________________________________________ ___________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Tue Aug 28 14:17:39 2001 Received: from email04.aon.at ([195.3.96.115]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7SIHcM03489 for ; Tue, 28 Aug 2001 14:17:39 -0400 Received: (qmail 184478 invoked from network); 28 Aug 2001 18:17:32 -0000 Received: from n784p005.adsl.highway.telekom.at (HELO pc1.eidolon.net) ([62.47.41.229]) (envelope-sender ) by qmail4.highway.telekom.at (qmail-ldap-1.03) with SMTP for ; 28 Aug 2001 18:17:32 -0000 Sender: hal@pc1.eidolon.net To: chemistry@CCL.net Subject: modifying (tuncating) basis sets? From: Hannes Loeffler Date: 28 Aug 2001 20:17:32 +0200 Message-ID: <87ae0k82wz.fsf@pc1.eidolon.net> Lines: 15 User-Agent: Gnus/5.0808 (Gnus v5.8.8) XEmacs/21.4 (Artificial Intelligence) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, I want to use the LANL2DZ for Cu(2+). Now, this basis set contains some diffuse functions which should be unnecessary for a cation. Some publications mention such truncated basis sets and some people in our lab also used to truncate basis sets. Well, I'm a little bit suspicious about such modifications. Should such modifications be done, i.e. is it safe? When should a function be considered as diffuse? (LANL2DZ for instance has three uncontracted (1 x s, 2 x p) functions with exponents that "look" small.) What about truncations in contracted functions? Hannes.