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<br><br><div class="gmail_quote">On Sat, Feb 25, 2012 at 12:09 PM, priya thiyagarajan <span dir="ltr"><<a href="mailto:priya.thiyagarajan09@gmail.com">priya.thiyagarajan09@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
hello sir,<br><br>i was performing simulation for 30ns.<br>due to queue time limit my mdrun stopped at 11.6ns.. then i extended my simulation using these two commands<br><br><b>tpbconv -s md.tpr -extend 20000 -o newmd.tpr<br>
</b></blockquote><div><br></div><div><br></div><div>I suppose you donot need to extend as the information to execute for 30ns is contained in the md.tpr. What you need to is to just include -cpi state.cpt while resubmitting your job. </div>
<div>i.e., </div><div><br></div><div><b>mdrun -s md.tpr -cpi state.cpt </b><b>-o md.trr -c md.gro -e md.edr -g md.log </b><b>-x traj.xtc</b></div><div><b><br></b></div><div><b><br></b></div><div>Chandan</div><div><br></div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><b>
<br>mdrun -s newmd.tpr -o md.trr -c md.gro -e md.edr -g md.log -cpi state.cpt -x traj.xtc -append<br></b><br><br>when i submit my mdrun<br>i got error as <br><br><br><br>Output file appending has been requested,<br>but some output files listed in the checkpoint file state.cpt<br>
are not present or are named differently by the current program:<br>output files present: md.log md.trr md.edr<br>output files not present or named differently: traj.xtc<br><br>-------------------------------------------------------<br>
Program mdrun, VERSION 4.5.5<br>Source code file: checkpoint.c, line: 2146<br><br>Fatal error:<br>File appending requested, but only 3 of the 4 output files are present<br>For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br><br><br><br>but i had traj.xtc file in my folder..<br><br><br>then again i checked my folder and again submitted my job..<br>
this time i got different error..<br><br>i dono why i am getting like this...<br><br>i got error as<br><br>Reading file newmd.tpr, VERSION 4.5.5 (single precision)<br>Starting 8 threads<br><br>Reading checkpoint file state.cpt generated: Fri Feb 17 19:46:58 2012<br>
<br><br><br>-------------------------------------------------------<br>Program mdrun, VERSION 4.5.5<br>Source code file: checkpoint.c, line: 1757<br><br>Fatal error:<br>Failed to lock: md.log. Function not implemented.<br>
For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br><br><br><br>
same command i used but i got different errors each time..<br>
<br>can anyone please help me with your answer..<br><br>i searched in users list.. but i didnt get the point..<br><br>please help with your answer.<br><br>thanking you,<br><br><br>
<br>--<br>
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