[gmx-users] Centering the system

Андрей Гончар gontchar at gmail.com
Wed Oct 16 14:35:40 CEST 2013

You should use the following command to center your protein:
trjconv -f trajectory.xtc -o corrected_trajectory.xtc -pbc mol -center -s
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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Andrew Gonchar
Андрей Гончар

More information about the gromacs.org_gmx-users mailing list