[gmx-users] problem with dimer simulation !

Kay Gottschalk kay.gottschalk at physik.uni-muenchen.de
Sat Sep 9 17:42:34 CEST 2006

try - cluster, and then as cluster group protein.

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!
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060909/9bc046ce/attachment.html>

More information about the gromacs.org_gmx-users mailing list