[gmx-users] problem with dimer simulation !

[Kay Gottschalk]

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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