[gmx-users] Extract only last frame from a trr
Dear gmx users, Probably a silly question, but I have been having some trouble finding an answer. I would like to use trjconv to extract the last snapshot from the trr trajectory of a crashed simulation. Thing is, I want to do it with a script and without knowing exactly when the simulation crashed, so I am looking for an option in trjconv that makes it go directly to the last frame. Another way to do it, since my calculations crash due to LINCS WARNINGS (which I know the reason for), would be to gently terminate the calculation when I get the first warning and print the corresponding gro file. Is there any way to do it? Thanks, Joan The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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.
[gmx-users] (no subject)
Dear gmx users, I am trying to extend a finished simulation from a frame which is not the last one in my trajectory. I have tried convert-tpr but I think it's only modifying the number of steps because the resulting tpr file starts the simulation from the first or the last frame depending on whether or not I supply the cpt file to mdrun. Is there any way to do what I am trying or is using grompp every time my only choice? Thanks, Joan The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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.
[gmx-users] gmx make_ndx: select last created group without knowing its number
Dear gmx users, I want to check how big are the biasing forces of a collective variable compared to the normal MD forces. As my collective variable only takes into account certain atoms of the system, I'd like to use make_ndx to create a group containing these atoms and give a name to that group so that I can use it later in a script The problem is that I am running this calculation for a lot of systems, some of them with ligands, some of them without, so I would like to use a script to create these groups for all my systems. As the number of the last created group will not always be the same, I was wondering if there is any option in make_ndx that allows to select the last group on the list so i can give it a suitable name without knowing its group number. Thanks, Joan The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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.
