Thanks Justin! it works now.<br><br>Greg<br><br><div class="gmail_quote">On Wed, Nov 3, 2010 at 7:39 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="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">----- Original Message -----<br>From: Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>><br>
Date: Thursday, November 4, 2010 10:38<br>Subject: Re: [gmx-users] extending simulation without cpt file<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>----- Original Message -----<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>From: Yongchul Chung <<a href="mailto:yxc169@case.edu" target="_blank">yxc169@case.edu</a>><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Date: Thursday, November 4, 2010 10:28<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Subject: [gmx-users] extending simulation without cpt file<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br></div><div><div></div><div class="h5"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>> </font>Hello gmxers,<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>> </font>I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but erased cpt file. However, I need to extend the simulation from the end of the trajectory file. I know this will not be binary identical as stated here (<a href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations" target="_blank">http://www.gromacs.org/Documentation/How-tos/Extending_Simulations</a>). I used following commands.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> <font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>> </font>tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>> </font>mdrun -s topolnew.tpr<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>> </font>When I do this and run the simulation, for some reason, the simulation starts from t=0 instead of t=102000. it seems like gromacs is writing the file without recognizing it that it should start the trajectory from 102000 ps. Is this a known bug? If so, is there a way around to solve this problem?<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br></div></div><div class="im"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>You've extended the run time of the original simulation, and forced it to start from the state in the new .tpr, but that state came from the original .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that of the checkpoint.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Your best chance of continuing will come from reconstructing the .mdp suitably (use gmxcheck to compare resulting .tpr files) and using grompp to create a .tpr using the most recent endpoint permitted by your .trr + .edr.<br>
<br></div>Actually, Justin's right. tpbconv needs -e -t files. It's been so long since I used it, I'd forgotten :-)<br><font color="#888888"> <br> Mark<br>
</font><br>--<br>
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