[gmx-users] Resuming of calculation from last *.cpt
jalemkul at vt.edu
Sat Sep 15 16:12:52 CEST 2012
On 9/15/12 10:11 AM, James Starlight wrote:
> yes, the initial files were named as the md_initial
> the simulation was resumed correctly but all output data was saved
> into new set of files with the default names. In my case I want that
> the resummed simulation data will write to the existing (md_initial)
> files without creation of new trajectory and other files.
mdrun -cpi -append -deffnm md_initial
Should do the trick.
> 2012/9/15 Justin Lemkul <jalemkul at vt.edu>:
>> On 9/15/12 10:03 AM, James Starlight wrote:
>>> In accordance to the manual I've re-launched my simulation by the command
>>> mpiexec -np 48 mdrun_mpi.openmpi -v -s md_initial -cpi md_initial
>>> where md_initial is the name of the files from the run which I want to
>>> As the result this produce new files with the default names traj.trr
>>> ener.edr etc. In those files the trajectory have been calculated from
>>> the last frame of the md_initial.cpt file. So as the result I've
>>> obtain again 2 set of output files ( from old and new runs). IS it
>>> possible to continue the calculations and save output within the
>>> existing files (md_initial) without creation of new ones ?
>> The names of the files produced depend on what is stored in the .cpt file.
>> mdrun will only append to files with those names. I don't have a clear
>> picture of what you've done so it's impossible to say whether or not this is
>> the expected outcome, but the checkpointing feature is very robust so I
>> suspect it is. Were all of your file names originally called md_initial?
>> If you've re-named them, the appending will fail for that very reason.
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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