[gmx-users] about protein in periodic boundary condition..

[Justin A. Lemkul]

rama david wrote:
> Hi GROMACS user,
>                           With the help of command
> genbox -ci <molecule name> -nmol <molecule no required>
>  -o <out put file> -box <dimension >
>  I get the desired no of added protein to cell.
>  But I found that some part of protein is outside 
> the cell ..
>    Is such system is good for further molecular dynamics study ...??
> 
>  After energy minimisation some time the protein is leaving the cell,
>  Can I used these last frame for my further position restrained MD
> study...???

There is no "outside" of a periodic cell.  This behavior is entirely normal.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-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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