[gmx-users] new molecule with non standard residues and its solvation

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Mon Jun 16 11:44:01 CEST 2003

jiri vondrasek wrote:
> Hi all
> I am quite unexperienced in GROMACS so the question is probably stupid.
> I am trying to simulate a molecule with non standard residues (about
> 300atoms) in solvent. The problem is that I do not know what kind and
> number of files I need for successful gromacs run. I have already
> created topology file and gro files at PRODRG. My question is - what's
> next? I am reading gmx manual and some tutorials - unfortunately I was
> not able to find any relevant information till now.Thanks

If you already have the topology of the molecule you have to create
a solvent box around it and get the simulation started.
Check out the speptide tutorial. Your problem sounds quite similar.

For further information about the options of the run input files
refer to chapter 7 in the manual.

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785

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