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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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