[gmx-users] quick question about restart

[Dallas Warren]

I use the second option there on all my simulations, using a script.  Simulations are done in 10ns blocks, at the completion of that the pbs script submits the next job.  Have found this way much less hassle, better computer utilisation etc.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Anna Marabotti
Sent: Wednesday, 29 February 2012 9:48 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] quick question about restart

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)

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? Which is the best preferred procedure?

Thank you very much
Anna
____________________________________________________
Anna Marabotti, Ph.D.
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm

"When a man with a gun meets a man with a pen, the man with a gun is a dead man"
(Roberto Benigni, about Roberto Saviano)

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