Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

update: I am trying using the way that you have suggested me # the first step gmx convert-tpr -s old.tpr -o new.tpr -extend 5 mdrun_mpi -s new.tpr -deffnm old -cpi old -append Here there is an issue: Each time all pieces of the files will be merged into "old" (.trr .edr and .cpt). But

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

Thanks Mark! assuming that I am interesting to obtain separate files for the each step I need just one command: mdrun -v -deffnm step7_1 -cpi step7_1.cpt -noappend that each time should create step7_1part002 etc but in case if I want to set manes of each pieces manually (it sounds crazy but in

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

Hi, There are some differences in recent GROMACS versions here (because the old implementations were not robust enough), but the checkpoint restart will not work with appending unless it finds the output files named in the .cpt match those on the command line (here, from -deffnm). You're making

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

thanks Mark! could you please also confirm that my method of the prolongation of the simulation would be correct #entend simulation for 50 ns and save these pieces as the separate files with the name step7_2* gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 5 mdrun -v -deffnm step7_2

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

Hi, The previous checkpoint has the _prev suffix, in case there is a problem that might require you to go further back in time. Mark On Fri, Jun 22, 2018, 10:46 Own 12121325 wrote: > P.S. what the difference between name.cpt and name_prev.cpt produced by > mdrun? What check-point should

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

P.S. what the difference between name.cpt and name_prev.cpt produced by mdrun? What check-point should correspond to the last snapshot in trr file ? 2018-06-22 10:17 GMT+02:00 Own 12121325 : > In fact there is an alternative trick :-) > If I rename a tpr file via gmx convert-tpr and then run

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

In fact there is an alternative trick :-) If I rename a tpr file via gmx convert-tpr and then run mdrun using this new tpr as well as previous checkpoint, it will produce all pieces of the trajectory in the separate file: gmx convert-tpr -s step7_1.tpr -o step7_2.tpr -extend 5 mpirun -np

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

On 6/21/18 2:35 AM, Own 12121325 wrote: and without append flag it will produce an output in the separate file, won't it? No, because appending is the default behavior. Specifying -append just invokes what mdrun does on its own. If you want a separate file, add -noappend to your mdrun

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

and without append flag it will produce an output in the separate file, won't it? gmx convert-tpr -s init.tpr -o next.tpr -extend 50 gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt 2018-06-21 1:12 GMT+02:00 Justin Lemkul : > > > On 6/19/18 4:45 AM, Own 12121325 wrote: > >> Hello Justin,

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

On 6/19/18 4:45 AM, Own 12121325 wrote: Hello Justin, could you specify please a bit more. Following your method, if the simulation has been terminated by crash without producing gro file so to re-initiate it I only need one command: gmx mdrun -s initial.tpr -cpi the_last_chekpoint.cpt

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

Hello Justin, could you specify please a bit more. Following your method, if the simulation has been terminated by crash without producing gro file so to re-initiate it I only need one command: gmx mdrun -s initial.tpr -cpi the_last_chekpoint.cpt -append where the last_checkpoint should be

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

On 6/18/18 9:11 AM, Own 12121325 wrote: thanks Justin for the suggestions! but generally this antiquated approach produces correct thermodynamical ensembles (since I do not call grompp again), doesn't it? Following this method the last snapshot from the trajectory will be taken to continue

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

thanks Justin for the suggestions! but generally this antiquated approach produces correct thermodynamical ensembles (since I do not call grompp again), doesn't it? Following this method the last snapshot from the trajectory will be taken to continue job, right ? 2018-06-15 14:22 GMT+02:00

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

On 6/14/18 4:01 AM, Own 12121325 wrote: Hello, I wonder to know if it's necessary to provide edr file for the completed part of the simulation in order to continue the md job assuming that I provide the trajectory (with coordinates and velocities) using gmx convert-tpr. Does the ensembles

[gmx-users] Continuation of the gromacs job using gmx convert-tpr

Hello, I wonder to know if it's necessary to provide edr file for the completed part of the simulation in order to continue the md job assuming that I provide the trajectory (with coordinates and velocities) using gmx convert-tpr. Does the ensembles produced by mdrun will be the same following