[gmx-users] restrained md_coordinate issue

zaved at tezu.ernet.in zaved at tezu.ernet.in
Fri Sep 22 13:49:13 CEST 2017

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


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