Thanks Justin !!<br>But my state_prev.cpt file shows <br>$gmxcheck -f state_prev.cpt<br><br>Checking file state_prev.cpt<br><br># Atoms 186864<br>Last frame -1 time 9346.700<br><br><br>Item #frames Timestep (ps)<br>
Step 1<br>Time 1<br>Lambda 1<br>Coords 1<br>Velocities 1<br>Forces 0<br>Box 1<br><br clear="all">Here also the time is greater than the .trr file.<br>
<br>Cant understand how to overcome it.<br><br>Chandan<br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Tue, Feb 16, 2010 at 11:02 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Chandan Choudhury wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Mark !!!<br>
Thanks for answering.<br>
My query is how do I restart my mdrun because the command<br>
nohup mpirun -np 16 -machinefile mac mdrun -s md5-10.tpr -cpi state.cpt -append &<br>
will not start from where the trajectory was stopped (i.e; time 9169.500). As this command will continue the simulation from where the cpt file was written.<br>
<br>
</blockquote>
<br></div>
Right, it will start from whenever the checkpoint was written. You should also have a state_prev.cpt that is a backup in case this type of thing happens; it may help. Regardless, with a 36-GB .trr file, the -append option will not work. Leave it out and use trjcat later.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
Any suggestions??<br>
<br>
chandan<br>
<br>
--<br>
Chandan kumar Choudhury<br>
NCL, Pune<br>
INDIA<br>
<br>
<br></div><div><div></div><div class="h5">
On Tue, Feb 16, 2010 at 9:36 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br>
On 17/02/10 02:52, Chandan Choudhury wrote:<br>
<br>
Hello gmxusers !!!<br>
I want to continue my simulation, from where the point where it<br>
stopped.<br>
The gmxcheck on .trr and cpt files are as:<br>
<br>
$gmxcheck -f state.cpt<br>
<br>
Checking file state.cpt<br>
<br>
# Atoms 186864<br>
Last frame -1 time 9362.500<br>
<br>
<br>
Item #frames Timestep (ps)<br>
Step 1<br>
Time 1<br>
Lambda 1<br>
Coords 1<br>
Velocities 1<br>
Forces 0<br>
Box 1<br>
<br>
$gmxcheck -f 5-10.trr<br>
<br>
Checking file 5-10.trr<br>
trn version: GMX_trn_file (single precision)<br>
Reading frame 0 time 5169.500<br>
# Atoms 186864<br>
Reading frame 8000 time 9169.500<br>
<br>
<br>
Item #frames Timestep (ps)<br>
Step 8395 0.5<br>
Time 8395 0.5<br>
Lambda 8395 0.5<br>
Coords 8395 0.5<br>
Velocities 8395 0.5<br>
Forces 0<br>
Box 8395 0.5<br>
<br>
<br>
There is a mismatch of time in both the outputs.<br>
<br>
The date of modification of both the files as shown are:<br>
<br>
Feb 15 19:55 state.cpt<br>
<br>
$date -r 5-10.trr<br>
Mon Feb 15 19:59:56 IST 2010<br>
<br>
The cpt file shows time greater than the trr file. But the time of<br>
modification of cpt file is less than trr file.<br>
<br>
<br>
If the simulation stopped catastrophically, then the timestamp could<br>
easily differ, especially if the .cpt is opened, written to and<br>
closed periodically, and the .trr is open continuously.<br>
<br>
<br>
Cannot understand the,<br>
how to restart the mdrun. And the size of the trr file is 36GB.<br>
Can I<br>
use the append flag in mdrun for gmx 4.0.5.<br>
<br>
<br>
Search the webpage for suggestions.<br>
<br>
Mark<br>
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</div></blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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