[gmx-users] [Fwd: free energy calculation]

David van der Spoel spoel at xray.bmc.uu.se
Thu Sep 17 15:16:20 CEST 2009

-------- Original Message --------
Subject: 	free energy calculation
Date: 	Wed, 16 Sep 2009 11:34:25 -0400
From: 	Elio Cino <ecino at uwo.ca>
To: 	spoel at gromacs.org

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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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