My idea is to do as suggested by van der Vegt in 1996JChPh.105.8849V. The attractive part of the LJ is turn off to avoid monomers from sticking together. Regards
Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -----Original Message----- From: [EMAIL PROTECTED] on behalf of Berk Hess Sent: Mon 7/3/2006 10:55 AM To: gmx-users@gromacs.org Subject: RE: [gmx-users] Compiling;Van der Waals: switch attractive term off >From: "Alessandro Mattozzi" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org> >To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> >Subject: RE: [gmx-users] Compiling;Van der Waals: switch attractive term >off >Date: Mon, 3 Jul 2006 10:40:18 +0200 > >Thanks! >How should I do it? Is force.c used by grompp or mdrun? I want to know if I >can run on shared resources (by just preprocessing with the edited version) >or I do have to run it locally. I think you did not answer to my question yet. For coarse-grained polymer models one usually sets the LJ force to zero after the minimum. But I don't know what you want to do exactly, so maybe you really want to turn of the 1/r^6 term. I that case it seems a bit complicated to me to edit Gromacs source code. For a simple polymer you just have a few LJ parameters, so I guess it is easier to just set all C6 parameters to zero in the force field file. If you use sigma and epsilon entries, it is little work to change these to C6/C12 values. The manual describes how to do this. Berk. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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