Yes, Mark. I now understand. I use united atom model. In my system, protein includes only methane pair. I still need those parameter to control protein/solvent, solvent/solvent interaction. Thanks so much for your great help. I will do it now.
Best, -Xianghong Qi On Wed, Nov 19, 2008 at 1:48 AM, Mark Abraham <[EMAIL PROTECTED]>wrote: > xianghong qi wrote: > >> Thanks, Mark. That means I can set energygrp_excl = Protein Protein, then >> I can get rid of those parameter which are related to electrostatics, Vdw( >> like rcoulomb, vdw-type, rvdw, rvdw-switch, etc). Am I right? >> > > No. Section 7.3.19 indicates how this should be done. I think you want > > energygrp_excl = Methane1 Methane2 > > so you will need to use make_ndx suitably to create these groups. > > If "Protein" includes only your pair of methanes, then > > energygrp_excl = Protein Protein > > will have the same effect, only because there are no intramolecular > nonbonded interactions in methane. It's thus not a generalizable solution... > > > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > -- Some people make the world more special just by being in it.
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