[gmx-users] trjconv -pbc/box /solvent

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 3 12:27:17 CET 2010

shahab shariati wrote:
> Dear Justin
> thanks for your attentions
> In my case, after md simulation my protein diffuse out from one side of 
> box. for solution I used trjconv -pbc nojump. then problem fixed but box 
> disappears and water molecules recedes from protein.

That sounds like the expected behavior.  The water molecules will appear to 
diffuse outward instead of jumping back to the other side of the box.  I 
generally find that trjconv -pbc mol -ur compact -center has a much better 
effect, for visualization purposes.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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