[Fwd: Re: Re: [MMTK] (no subject)]

mprabha at fiu.edu mprabha at fiu.edu
Mon Dec 12 12:58:32 CET 2005


> 
> From: <mprabha at fiu.edu>
> Date: 2005/12/12 Mon AM 06:57:47 EST
> To: khinsen at cea.fr
> Subject: Re: Re: [MMTK] (no subject)
> 
> Do you have any demo  verson for protein simulation.
> the example bala1 does not contain minimization
> thank you
> prabhakaran
> > 
> > From: khinsen at cea.fr
> > Date: 2005/12/12 Mon AM 05:44:34 EST
> > To: <mprabha at fiu.edu>
> > CC: mmtk at python.net
> > Subject: Re: [MMTK] (no subject)
> > 
> > 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.
> > --
> > ---------------------------------------------------------------------
> > 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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