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>Any suggestions??<br><br>chandan<br clear="all"><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Tue, Feb 16, 2010 at 9:36 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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><div></div><div class="h5">On 17/02/10 02:52, 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;">
Hello gmxusers !!!<br>
I want to continue my simulation, from where the point where it 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>
</blockquote>
<br></div></div>
If the simulation stopped catastrophically, then the timestamp could easily differ, especially if the .cpt is opened, written to and closed periodically, and the .trr is open continuously.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Cannot understand the,<br>
how to restart the mdrun. And the size of the trr file is 36GB. Can I<br>
use the append flag in mdrun for gmx 4.0.5.<br>
</blockquote>
<br></div>
Search the webpage for suggestions.<br>
<br>
Mark<br><font color="#888888">
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