[gmx-users] quick question about restart

[Anna Marabotti]

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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