[gmx-users] Resuming of calculation from last *.cpt

James Starlight jmsstarlight at gmail.com
Sat Sep 15 16:11:58 CEST 2012


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.


2012/9/15 Justin Lemkul <jalemkul at vt.edu>:
> On 9/15/12 10:03 AM, James Starlight wrote:
>> Justin,
>> 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
>> -append
>> where md_initial is the name of the files from the run which I want to
>> continue.
>> 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
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list