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

[Justin A. Lemkul]

shahab shariati wrote:
> Dear Justin
>  
> in my case only -pbc nojump fix problem. my purpose is not 
> visualization. do this xtc file ,in which protein diffuse out from box, 
> cause any problem in analysis? if yes, how can I fix it?
>  
>

This same question has come up several times within the last week or two. 
Please check the archives for more details, but most Gromacs tools handle PBC 
internally.  Some tools do not (g_rms, g_gyrate, etc), requiring PBC correction.

-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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