<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
That's enough for the non-bonded interactions.<br>Energy group exclusions work on both the energy and the forces.<br>But if you have bonded interactions between atoms in S you also need to exclude those.<br>Note that this only matters if you want to have the pressure.<br><br>Berk<br><br>> From: yelash@uni-mainz.de<br>> To: gmx-users@gromacs.org<br>> Date: Thu, 27 Aug 2009 16:13:42 +0200<br>> Subject: RE: [gmx-users] Pressure for froozen atoms<br>> <br>> Hi together,<br>> <br>> > You have to make sure that you do not calculate forces between frozen atoms,<br>> <br>> is it enough to include in grompp.mdp such command:<br>> <br>> ; Non-equilibrium MD stuff<br>> freezegrps = S <br>> freezedim = Y Y Y<br>> <br>> ;Energy group exclusion for position restraints<br>> energygrps = A S<br>> energygrp_excl = S S<br>> <br>> Or it excludes only energy calculations, but not forces?<br>> <br>> Regards,<br>> Leonid<br>> <br>> ________________________________________<br>> From: gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] On Behalf Of Berk Hess [gmx3@hotmail.com]<br>> Sent: Thursday, August 27, 2009 2:59 PM<br>> To: Discussion list for GROMACS users<br>> Subject: RE: [gmx-users] Pressure for froozen atoms<br>> <br>> Hi,<br>> <br>> Gromacs does not do anything special for frozen atoms.<br>> You have to make sure that you do not calculate forces between frozen atoms,<br>> if you want the virial to be correct.<br>> <br>> Berk<br>> <br>> > Date: Thu, 27 Aug 2009 14:46:47 +0200<br>> > From: alexander.herz@mytum.de<br>> > To: gmx-users@gromacs.org<br>> > Subject: [gmx-users] Pressure for froozen atoms<br>> ><br>> > Hi guys,<br>> ><br>> > does gromacs use the following scheme to calculate the virial/pressure<br>> > for systems including froozen atoms:<br>> > http://www.ccp5.ac.uk/infoweb/wsmith22/wsmith22/wsmith22.html<br>> > ??<br>> ><br>> > Thx,<br>> > Alex<br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> ________________________________<br>> See all the ways you can stay connected to friends and family<http://www.microsoft.com/windows/windowslive/default.aspx><br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
</html>