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<div>Yes it is, or should be from my experience. You need to look at the mailinglist, and it takes time t work out somethings as there also system (your simulation) dependent. Mostly these are parameters such as domain decomposition sizes, number of threads, -rdd, -rcon -dds and others (I found more important for speed) -mpi vs -nt and -ntomp and similar parameters, along with some -npme. The mail list has alot more, but in the end these have to be optimised based on your system, deminsions, whats in it, etc...in the end you see a speed up untill you get a good 200 atoms per unit cell in the decomposed grid is what I found, a 4-5 day simulation, 4000 amino acids and 169,000 atoms went to 12-15 hours at 4-5 ns simulation time.</div>
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<div>Sincerely,</div>
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<div>STephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Donnerstag, 30. Januar 2014 um 19:50 Uhr<br/>
<b>Von:</b> "MUSYOKA THOMMAS" <mutemibiochemistry@gmail.com><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> [gmx-users] MD SIMULATIONS ON A CLUSTER</div>
<div name="quoted-content">Dear Users,<br/>
I have been doing 10 ns MD simulations of protein-ligand complexes on a<br/>
local cluster of 64 cores using GROMACS 4.5.7. However, there seems to be<br/>
no much difference in the time it takes to complete one cycle of an mdrun<br/>
(3-days - same as when I used a machine with 4 cores).<br/>
<br/>
Will be appreciative to know if its possible shorten the time period.<br/>
<br/>
See the following command that I have incorporated in a python script so as<br/>
to automate the md process right from the beginning.<br/>
<br/>
<br/>
md="md.mdp"<br/>
os.system(mdscriptcopy)<br/>
finalmdruncommand="grompp -f %s -c %s -t %s -p %s -n %s -o %s"%<br/>
(md,nptgro,nvtcpt,topoltop,indexfile,mdtpr)<br/>
os.system(finalmdruncommand)<br/>
*finalrun="mdrun -v -deffnm md"*<br/>
os.system(finalrun)<br/>
<br/>
<br/>
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<br/>
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