[gmx-users] Centering the system

[Андрей Гончар]

Hi.
You should use the following command to center your protein:
trjconv -f trajectory.xtc -o corrected_trajectory.xtc -pbc mol -center -s
trajectory.tpr
Don't forget to replace "trajectory" with corresponding filenames


2013/10/16 Shima Arasteh <shima_arasteh2001 at yahoo.com>

>
>
> Dear gmx users,
>
> I have a system consist of a lipid bilayer and a peptide. As the initial
> configuration, the peptide is located in center of the x-y plane above
> lipid bilayer. After running MD, the peptide shows interactions with the
> polar groups. It's ok, but the peptide is near one edge of the x-y plane of
> the bilayer. I' d like to know if there is any way to use the properties of
> the pbc and see the peptide in center of the x-y  plane while interacting
> with the polar groups?
>
> Thanks in advance,
> Your suggestions would be appreciated.
>
> Sincerely,
> Shima
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-- 
Andrew Gonchar
Андрей Гончар