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

[Justin A. Lemkul]

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

-- 
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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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