[gmx-users] restrained md_coordinate issue

[Mark Abraham]

Hi,

Restraints don't freeze the coordinates, you must expect movement.

Mark

On Fri, 22 Sep 2017 13:49 <zaved at tezu.ernet.in> wrote:

> Hello Everyone
>
> I have simulated a protein - ligand complex with gromacs 5.1.4 for 100ns.
>
> I have restrained the position of the ligand ( which in my case is
> hydrogen peroxide).
>
> Applied following commands for correcting pbc:
>
> gmx_mpi trjconv -f md.xtc -s md.tpr -pbc -nojump -o file1.xtc
>
> gmx_mpi trjconv -f file1.xtc -pbc mol -center -o file2.xtc
>
> After correcting the pbc effect, the coordinates of my ligand changes
> throughout the simulation (which should not be the case).
>
> I would also like to mention that the coordinates of my ligand in the
> md.xtc is fixed.
>
> But after applying above 2 commands, the ligand coordinates changes.
>
> Can't understand what's wrong!!!
>
> Any suggestion is appreciated.
>
> Thank You
>
> Regards
> Zaved
>
>
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