[gmx-users] (no subject)

Erik Lindahl lindahl at stanford.edu
Tue Mar 5 20:19:56 CET 2002

On Tue, 2002-03-05 at 10:45, Atom News wrote:
> Hi,
> I'am a new GROMACS user. I start to simulate a peptide. The pdb file of the 
> peptide is taken from MOLDEN. The coordinates of atoms are defined in the 
> unit of A^o. I converted these to nm (GROMACS's unit) but after energy 
> minimization, I got a very large energy and the minimization did not 
> converge. Can anyone offer a help?
> John

Hi John,

 From your mail I get the impression that you manually converted measures
from AA to nm? You definitely shouldn't do that - the pdb file format
standard specifices AA and not nm, and any conversion will be taken care
of automatically. If you're changing things in the pdb file you'll end
up with coordinates that are a factor 10 too large.

You can find a suggested workflow for pdb files in the getting started
section of the documentation at http://www.gromacs.org



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