From owner-nwchem-users Mon May 20 14:08:19 2002 Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.8.8+Sun/8.8.5) id NAA11727 for nwchem-users-outgoing; Mon, 20 May 2002 13:53:40 -0700 (PDT) Date: Mon, 20 May 2002 13:52:51 -0700 (PDT) From: Mohanraj Rajendran Subject: Free energy computation using Thermodynamic Integration To: nwchem-users@emsl.pnl.gov Message-id: <20020520205251.77926.qmail@web12906.mail.yahoo.com> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Hello NWchem users, I am interested in computing free energy changes using molecular dynamics. In the example files that come with NWChem 4.0.1, the examples 'na_k' (nak_ti.nw) and 'ethanol' (ethanol_ti.nw) use the molecular dynamics directive task md thermodynamics for free energy computation through thermodynamic integration/perturbation. The output files ethanol_ti.out and nak_ti.out contain some 'nan' entries and I do not know how well the code works for thermodynamic integration. In the 'na_k' case the free energy change associated with the mutation Na+ --> K+ is estimated to be around 32 kcal/mol in the NWchem example. Is this a good estimate? When I run the input file nak_ti.nw, the code stops with the message "Deviation too large for solvent". In the NWchem message archive, a reply to a question involving this message suggests that a system optimization may help. Performing a lengthy equilibration helps only in some cases of free energy computation. What am I doing wrong? I am interested in knowing the experience of other users in performing free energy computations. Sample input files will be quite helpful. Thanks Raj Mississippi State University __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com