On 16/09/2012 12:17 AM, James Starlight wrote:
In that case I've obtain error
Fatal error:
Failed to lock: md_init.log. Already running simulation?
What does it means ? the md_init.log is present in the wor dir
Appending to an old run requires that all the filenames are identical
between the two runs. It looks to me like your .log file was called
md_init.log originally. You can use gmxdump -cp on your checkpoint file
to see what the output filenames used to be, and thus what they must now
be called if you want to use appending.
Mark
2012/9/15 Justin Lemkul <jalem...@vt.edu>:
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 <jalem...@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@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-requ...@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
========================================
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
