Hii Everyone I had performed a 100ns protein-ligand (docked complex) simulation with gromacs 5.1.4.
The ligand in my case is hydrogen peroxide. I have removed the PBC effect and centered the protein. I have used the following commands: gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o out.xtc gmx_mpi trjconv -f out.xtc -s md.tpr -pbc mol -center -o out_1.xtc I am analyzing the average distance between the protein and the ligand. I am getting a value of 3.2nm which is too high. Also in the out_1.xtc, after 10ns itself the ligand is moving all around the protein. Unable to understand why its happening!! Please suggest. Thank You Regards Z. Hazarika Research Scholar Tezpur University Tezpur, India * * * 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.
