[MMTK] (no subject)

khinsen at cea.fr khinsen at cea.fr
Mon Dec 12 11:44:34 CET 2005

On Dec 10, 2005, at 14:55, <mprabha at fiu.edu> wrote:

> I tried to run simulation 1CF3.pdb. I tried with example
> bala1 in examples.But the program stagnates showing potential  
> energy nan. Do you have any demo file for protein
> similar to demo file in GROMACS

I don't know the demo file in Gromacs, sorry...

If you get Nan for the energy, then you have either undefined  
positions in your system or positions that are Nan themselves. If  
this happens in the course of a minimization or molecular dynamics  
run, the most frequent cause is an inappropriate choice of parameters  
(e.g. heating a system too fast). You have to follow the log output  
and/or the trajectory file to see where things start to go wrong.  
Usually there is a strong increase or decrease in the potential  
energy before it becomes Nan.

Konrad Hinsen
Laboratoire Léon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: khinsen at cea.fr

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