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 sinc
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
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 ex
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 -cp
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 corres
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 mdr
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 ${NB
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 comm
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,
>>
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 -appe
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 somet
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 j
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 Justi
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 pr
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 th
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