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

[Justin Lemkul]

On 9/15/12 10:11 AM, James Starlight wrote:
> Jusin,
>
> 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.

-Justin

> James
>
> 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

-- 
========================================

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

========================================