Hi, Mark: I made the index file and call two methanes as methane1 and methane2 , then I set energygrp_excl = methane1 methane2, but when I run grompp, it said methane1 is not an energy group. What do you understand this problem? Thanks. -Xianghong Qi
On Wed, Nov 19, 2008 at 2:17 AM, xianghong qi <[EMAIL PROTECTED]>wrote: > 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. > -- Some people make the world more special just by being in it.
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