Re: [gmx-users] PBC after energy minimization
On 5/1/20 9:29 AM, John Whittaker wrote: 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. "Trajectories" from energy minimization are generally unreadable as the interval of saved frames is uneven. During EM, a frame is only written when the energy goes down, which is not necessarily every possible frame. I also seem to recall that there is never XTC output from EM, even if requested, because it's rather pointless. Maybe that has changed. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
Re: [gmx-users] PBC after energy minimization
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.
