[gmx-users] problem with volume equilibration

Kowsar Bagherzadeh kw_bagherzadeh at yahoo.com
Tue Jan 31 07:33:30 CET 2012

You'd better first your .top file, to see if you have included DPPC .itp file and also in the compound section. if it was ok, check the .ndx and look for the atom numbers of DPPC, after finding the atom numbers, make a group ( Like othe parts of .ndx; water, or protein,...) and name it DPPC. save and continue. Hope it help

From: Anushree Tripathi <anushritripathi at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, January 31, 2012 9:44 AM
Subject: [gmx-users] problem with volume equilibration

When I run the command (i.e., grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr)for volume equilibration.

I am getting the error:
Fatal error:
Group DPPC not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.
In that case use the '-n' option.

Please guide me.

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