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 * * * 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 posting! * 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-requ...@gromacs.org.
