[gmx-users] Fwd: -pbc nojump

[Carsten Kutzner]

On Oct 27, 2010, at 10:05 AM, leila karami wrote:

> Hi Carsten
>  
> Thanks for your answer. You got my case very well.
>  
> I understand your mean as follows:
> 
> 1)      Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol  (output group=water)
> 
> 2)      Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc nojump (output group =protein-dna)
> 
> Is that true?
Yes, I would try it that way.
> 
> You said, (Then overlay both results in the visualization program). How?
In pymol for example, just load both PDBs. 

Carsten