[gmx-users] problem with dimer simulation !

Daniela S. Mueller d.s.mueller at rug.nl
Mon Sep 11 05:39:43 CEST 2006

hi cw,

using trjconv -pbc nojump should remove the jumps. then you can analyse 
interactions between different chains, while it doesn't matter for the 
analysis where they diffuse.


Kay Gottschalk wrote:
> try - cluster, and then as cluster group protein.
> Kay.
> On Sep 9, 2006, at 11:09 AM, C.W. Liang wrote:
>> hi, all user:
>> i performed the dimer simulation,  and want to realize the interaction 
>> between two peptides.
>> but frequently, i  encountered this kind of problem:  sometimes 
>> peptides moved out of the box, and sometimes they jumped back.
>> i have tried so many way to pull them back with trjconv command, but 
>> still cause some unexpected problem.
>> for example, peptides break to many parts ( with -pbc whole ) 
>> or diffuse out of box gradually ( with -pbc nojump )
>> with -ur or -center still not the trajectory i really want. i 
>> think maybe there are some tricks to perform.
>> any suggestions for me ?   thanks sooooooooooo much!


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Daniela S. Mueller

Biologist (Dipl. Biol.)

- Molecular Dynamics Group, UQ -

School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
University of Queensland
Qld 4072, Brisbane

Phone: +61-7-33653732

Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm


- MD group, RuG -

Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

Website: http://www.rug.nl/gbb/md

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