On 29/02/2012 9:47 PM, Anna Marabotti wrote:
Dear gmx-users,
I'm running my simulations on a machine with a queue system that stops
the runs longer than 24 hours. Often, for my simulations, I need a
longer time to complete the runs. Let's have an example. I have to run
a 100ns-long simulation on a machine that produces 10ns/days
simulation. I have two possibilities:
First approach:
I'm setting within the .mdp file a global duration of 100 ns. Then:
grompp -f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr
mdrun -s input_fullMD.tpr -deffnm output_fullMD
After 24 h, I see that the run has been stopped after 10 ns. I have
the output_fullMD.cpt file. Then, I do:
mdrun -s input_fullMD.tpr -cpi output_fullMD.cpt -deffnm output_fullMD_2
and so on for 10 days, until the run has been completed (then I will
concatenate the .xtc, .edr, .trr files)
Yep, or use the same -deffnm filename and -append for more simplicity.
See http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#section_2
Second approach:
I'm setting within the .mdp file a global duration of 10 ns. Then (as
above):
grompp -f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr
mdrun -s input_fullMD.tpr -deffnm output_fullMD
After 24 h, the run has been finished. Then, I continue the run for
other 10 ns with:
tpbconv -s input_fullMD.tpr -extend 10000 -o input_fullMD_2.tpr
mdrun -s input_fullMD_2.tpr -cpi output_fullMD.cpt -deffnm output_fullMD_2
and so on for 10 days, until the 100-ns run has been completed.
Are the two procedure producing EXACTLY the same results, or not?
In principle, they are implementing the same algorithm over the 10 runs.
In practice, the discussion at
http://www.gromacs.org/Documentation/Terminology/Reproducibility applies
and you will likely not observe an identical trajectory from each case.
In theory, mdrun -reprod does a better job in many cases for often
losing performance, but random number states are not preserved, so
various algorithms cannot be reproducible across restarts.
Which is the best preferred procedure?
The first, with appending, is simple and requires no concatenation
post-processing. Feel free to back up your files between runs if you
want insurance against loss - but you should do that anyway.
Anything else requires you to do more work later on for no gain.
Mark
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