-------- Original Message -------- Subject: free energy calculation Date: Wed, 16 Sep 2009 11:34:25 -0400 From: Elio Cino <[email protected]> To: [email protected] Hello. Dr. van der Spoel. I have been waiting for an account to be made on gmx-users so that i can post. Until the account is made, I hope that you do not mind me sending you a question directly. I am trying to run free energy calculations on a protein - protein complex. I believe that I have made all of the necessary changes to my topology, and the nonbonded parameters are set to 0 for state B. I am using the GROMOS96 53a6 ff. My system runs fine with free energy turned off, but gives many lincs warnings when it is turned on, and lambda = 0 to 0.5. Ultimately the run crashes. The thing that I can think of that may be a problems is that state B has a nonzero charge, while A is 0. I have attached my run input, and topology. Any help is very much appreciated. Thanks. Elio Cino -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [email protected] [email protected] http://folding.bmc.uu.se
md_thermo.mdp
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2z32_B.itp
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