From owner-chemistry@ccl.net Sun Aug 7 10:05:19 2005 From: "CCL" To: CCL Subject: CCL: g98 vs g03 CPCM solvation energy Message-Id: <-28952-050806201207-17747-jTKKlThOvCLwkE03HCXsVw:_:server.ccl.net> X-Original-From: Marcin Krol Content-Type: TEXT/PLAIN; charset=US-ASCII MIME-Version: 1.0 Sent to CCL by: Marcin Krol Dear All, I want to calculate pKa values of some organic compounds. To start with I tried to repeat calculations already published for substituted phenyls (JACS 124(6421)). The authors used CPCM continuum solvation method with defaults settings implemented in g98 to optimize structures of molecules and get solvation free energy. The result they got for the phenoxide anion was -73.49 kcal/mol which agrees well with experimental data. I repeated their calculations using g03 and CPCM model and for the phenoxide anion got dG solv = -70.76 kcal/mol. Then I took g98 geometry and run SP calculation and again got dG ~ -70.5 kcal/mol. However, when I run calculations in g98 I got reported energy. There must be a change in the default parameters of the CPCM (or the method itself) in g98 and g03. Could you, please, tell me how to get the g98 CPCM in g03? Any comments are welcome. Thank you in advance marcin Dr Marcin Krol Zaklad Bioinformatyki Collegium Medicum UJ Kopernika 7E 31-501 Krakow, POLAND tel/fax (012) 422-77-64 e-mail mykrol:_:cyf-kr.edu.pl From owner-chemistry@ccl.net Sun Aug 7 15:18:43 2005 From: "CCL" To: CCL Subject: CCL: NAMD 2.6b1 (Parallel MD) Release Message-Id: <-28953-050805191633-28429-jTKKlThOvCLwkE03HCXsVw:+:server.ccl.net> X-Original-From: Jim Phillips Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed MIME-Version: 1.0 Sent to CCL by: Jim Phillips Dear CCL, NAMD is a molecular dynamics program, file compatible with X-PLOR, CHARMM, and AMBER, scalable to hundreds of processors, and available as source code or binaries for a variety of platforms, free of charge. Try it out! It's been a long time coming, but 2.6b1 is ready to go. This is a beta, so be on the lookout for bugs. I've added a page to the NamdWiki at http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?Namd26b1Release so please check that page and add any issues you may find. Thanks! -Jim +--------------------------------------------------------------------+ | | | NAMD 2.6b1 Release Announcement | | | +--------------------------------------------------------------------+ July 30, 2005 The Theoretical and Computational Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.6b1 has several advantages over NAMD 2.5: - Ports to Itanium, Altix, and Opteron/Athlon64/EMT64. - Improved serial performance on POWER and PowerPC. - Adaptive biasing force free energy calculations. - Tcl-based boundary potentials. - Reduced memory usage for unusual simulations. - Support for OPLS force field. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. For your convenience, NAMD has been ported to and will be installed on the machines at the NSF-sponsored national supercomputing centers. If you are planning substantial simulation work of an academic nature you should apply for these resources. Benchmarks for your proposal are available at http://www.ks.uiuc.edu/Research/namd/performance.html The Theoretical and Computational Biophysics Group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd:+:ks.uiuc.edu. We are eager to hear from you, and thank you for using our software!