[gmx-users] problem with dimer simulation !

C.W. Liang petrucci86 at vip.sina.com
Sat Sep 9 11:09:32 CEST 2006

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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