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<DIV><FONT size=2 face=Arial><SPAN class=194583010-29022012>Dear
gmx-users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=194583010-29022012>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.
</SPAN></FONT><FONT size=2 face=Arial><SPAN class=194583010-29022012>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:</SPAN></FONT></DIV>
<DIV><SPAN class=194583010-29022012><FONT size=2
face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN class=194583010-29022012><FONT size=2 face=Arial>First
approach:</FONT></SPAN></DIV>
<DIV><SPAN class=194583010-29022012><FONT size=2 face=Arial>I'm setting within
the .mdp file a global duration of 100 ns. Then:</FONT></SPAN></DIV>
<DIV><SPAN class=194583010-29022012><FONT size=2 face=Arial>grompp -f param.mdp
-c prot.gro -p topol.top -o input_fullMD.tpr</FONT></SPAN></DIV>
<DIV><SPAN class=194583010-29022012><FONT size=2 face=Arial>mdrun -s
input_fullMD.tpr -deffnm output_fullMD</FONT></SPAN></DIV>
<DIV><SPAN class=194583010-29022012><FONT size=2 face=Arial>After 24 h, I see
that the run has been stopped after 10 ns. I have the
output_fullMD.cpt file. Then, I do:</FONT></SPAN></DIV>
<DIV><SPAN class=194583010-29022012><FONT size=2 face=Arial>mdrun -s
input_fullMD.tpr -cpi output_fullMD.cpt -deffnm
output_fullMD_2</FONT></SPAN></DIV>
<DIV><SPAN class=194583010-29022012><FONT size=2 face=Arial>and so on for 10
days, until the run has been completed (then I will concatenate the .xtc, .edr,
.trr files)</FONT></SPAN></DIV>
<DIV><SPAN class=194583010-29022012><FONT size=2
face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN class=194583010-29022012><FONT size=2 face=Arial>Second
approach:</FONT></SPAN></DIV>
<DIV><SPAN class=194583010-29022012><FONT size=2 face=Arial>I'm setting within
the .mdp file a global duration of 10 ns. Then (as above):</FONT></SPAN></DIV>
<DIV><SPAN class=194583010-29022012><FONT size=2 face=Arial>
<DIV><SPAN class=194583010-29022012><FONT size=2 face=Arial>grompp -f param.mdp
-c prot.gro -p topol.top -o input_fullMD.tpr</FONT></SPAN></DIV>
<DIV><SPAN class=194583010-29022012><FONT size=2 face=Arial>mdrun -s
input_fullMD.tpr -deffnm output_fullMD</FONT></SPAN></DIV>
<DIV><SPAN class=194583010-29022012>After 24 h, the run has been finished. Then,
I continue the run for other 10 ns with:</SPAN></DIV>
<DIV><SPAN class=194583010-29022012>tpbconv -s input_fullMD.tpr -extend 10000 -o
input_fullMD_2.tpr </SPAN></DIV>
<DIV><SPAN class=194583010-29022012>mdrun -s input_fullMD_2.tpr -cpi
output_fullMD.cpt -deffnm output_fullMD_2</SPAN></DIV>
<DIV><SPAN class=194583010-29022012>and so on for 10 days, until the 100-ns run
has been completed.</SPAN></DIV>
<DIV><SPAN class=194583010-29022012></SPAN> </DIV>
<DIV><SPAN class=194583010-29022012>Are the two procedure producing EXACTLY the
same results, or not? Which is the best preferred procedure? </SPAN></DIV>
<DIV><SPAN class=194583010-29022012></SPAN> </DIV>
<DIV><SPAN class=194583010-29022012>Thank you very much</SPAN></DIV>
<DIV><SPAN class=194583010-29022012>Anna</SPAN></FONT></SPAN></DIV></DIV>
<DIV><SPAN class=194583010-29022012></SPAN><FONT size=2
face=Arial>____________________________________________________</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web page: <A
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 face=Arial>"When a man with a gun meets a man with
a pen, the man with a gun is a dead man"</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>(Roberto Benigni, about Roberto
Saviano)</FONT></DIV>
<DIV> </DIV></BODY></HTML>