Hi Mohamed, > Hello everybody, > > In order to solve the PBC at the end I use the command: > > *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * > > followed by: > > *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* > > > I want to solve this problem after the energy minimization but I don't > have > .xtc file to use it as I do at the end. > > How can I solve this problem after the energy minimization ?
You're saying that your energy minimization does not produce a trajectory (a .trr or .xtc file)? If that's the case, you just have to instruct GROMACS to periodically write to a trajectory file using options in the .mdp file (namely, nstxout). Take a look at: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html Under the section "output control" you will find what you are looking for. - John > > Thanks, > Mohamed > -- > 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. > ---------------------------------------- John Whittaker Ph.D. Candidate Department of Mathematics and Computer Science Freie Universität Berlin +49 0160 936 04221 -- 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.