[gmx-users] restrained md_coordinate issue
mark.j.abraham at gmail.com
Tue Sep 26 00:45:20 CEST 2017
Restraints don't freeze the coordinates, you must expect movement.
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
> * * * D I S C L A I M E R * * *
> This e-mail may contain privileged information and is intended solely for
> the individual named. If you are not the named addressee you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately by e-mail if you have received this e-mail in error and destroy
> it from your system. Though considerable effort has been made to deliver
> error free e-mail messages but it can not be guaranteed to be secure or
> error-free as information could be intercepted, corrupted, lost, destroyed,
> delayed, or may contain viruses. The recipient must verify the integrity of
> this e-mail message.
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users