Hi, Please check out the GROMACS FAQs. Your protein can't come out of a periodic cell
Mark On Thu, 3 Aug 2017 10:26 <za...@tezu.ernet.in> wrote: > Hello > > I had performed a 100ns protein simulation with gromacs 5.1.4. > > After the simulation I observed that the protein is coming out of the box. > > I have used the following commands to correct it: > > gmx_mpi trjconv -f md.xtc -s md.tpr -pbc mol -ur compact -center -o out.xtc > > gmx_mpi trjconv -f out.xtc -s md.tpr -dt 100 -o file.pdb > > Part of the protein is still out of the box (in the file.pdb). > > Please suggest. > > 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 > 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. > -- 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.