[MMTK] mmtk & vmd

mprabha@fiu.edu mprabha at fiu.edu
Tue Jan 24 15:01:36 CET 2006


thank you for the information
The simulation for 1CF (protein alone) runs smoothly.
It takes 55 minutes of a lnux  computer (red hat 9.0)
for 1 ps. If any body need , i can forwrad the entire steps
1) amber force filed formation
2) hydrogen addition
3) minimization 
4) heating & equilibration
5) prodiction run
6) restart information
7) visulization
8) trajectory analysis using xMoldyn

thnak you
prabha karan
> 
> From: khinsen at cea.fr
> Date: 2006/01/23 Mon AM 05:28:32 EST
> To: <mprabha at fiu.edu>
> CC: MMTK mailing list <mmtk at python.net>
> Subject: Re: [MMTK] mmtk  & vmd
> 
> On Jan 20, 2006, at 19:29, <mprabha at fiu.edu> wrote:
> 
> > I want to use vmd as visualiser for mmtk trajectory. when I run  
> > pthon visulaiser, it does not recognize vmd in the /usr/bin. Should  
> > i add any import statement in the python module. or set the  
> > environment varial in the cshell script
> 
> What you have to do is put
> 
> 	setenv PDBVIEWER /usr/bin/vmd
> 
> in ~/.cshrc.
> 
> 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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