[gmx-users] group by atom type in .GRO ?

erwin berthier erwindownunder at gmail.com
Tue Jul 25 01:11:10 CEST 2006

Hello I have a system with Lipids, gold and solvent. I generate the
.gro file myself with a script. Should I group the molecules together,
ie the lipids first then the gold and the solvent after, or can they
be all mixed up?
The errors I get right now is the following:
Warning: atom names in topol.top and conf.gro don't match (Au - HS1)
(and there is many of them)
I am sure my .itp file works because I have tested it independantly
with simple systems...

Moreover I wanted to ask also what is better to make an energy
minimization by blocking a group of the atoms. Should I use a freeze
group or position restraints ? I should add that I don't really care
if the atoms move around a little.

Many thanks
Erwin Berthier

PhD student
University of Canterbury
Electrical Engineering department
New Zealand
erwindownunder at gmail.com
+64 (0)3 3667001 + ext 7123

More information about the gromacs.org_gmx-users mailing list