Thanks! It really is. For the input cpt may have been overwritten before, when I put it in mdrun again..<br><br><br><div class="gmail_quote">2010/12/17 Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span><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"><br><br><span>On 12/17/10, <b>Qin Qiao </b> <<a href="mailto:qiaoqin47@gmail.com" target="_blank">qiaoqin47@gmail.com</a>> wrote:</span><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite">
<div>Thanks! <br><br>But still sth strange: I found the total energy is not identical between the last frame of the previous REMD and the first frame of the next REMD in one replica. <br><br>last frame of the previous: 500.000000 -372343.906250<br>
first frame of the next: 0.000000 -361778.375000<br><br>I wonder whether there's some problem and what caused it..</div></blockquote><br></div>OK, we'll need to see the exact sequence of commands that produced your observations, i.e. mdrun, then tpbconv, then mdrun. The fact that you're managing to get the time reset to zero indicates you've done something wrong. As a guess, you didn't use the right .cpt file with the second mdrun -cpi.<div class="im">
<br><br><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div><br><br>My setting<br>In the .mdp of the previous simulation, gen_vel was on; I didn't record the velocity by putting nstvout =0; I used xtcgrp = Protein. </div>
</blockquote><br></div>These don't matter.<br><font color="#888888"><br>Mark</font><div><div></div><div class="h5"><br><br><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite">
<div><br>Best<br><br>Qin<br><br><div class="gmail_quote">2010/12/15 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><div><br></div><div><br>
<br>
Qin Qiao wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Sir or Madam,<br>
<br>
I wonder how to continue a REMD running using .cpt file in Gromacs 4.5.1. Since I ran a REMD of 56 replicas, there are one cpt file for each replica.. I couldn't do it by<br>
<br>
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr<br>
<br>
mdrun -s next.tpr -cpi previous.cpt<br>
<br>
<br>
I guess it's not for an iterative line in the answer in <a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg33566.html" target="_blank">http://www.mail-archive.com/gmx-users@gromacs.org/msg33566.html</a>, since the mdrun should run simultaneously.<br>
<br>
</blockquote>
<br></div></div>
The iterative approach Mark describes in that post is for the tpbconv step. Simply extend all of your .tpr files to generate new ones (iterate over all your .tpr files), then proceed with mdrun as you would normally, making use of the -cpi feature.<br>
<br>
-Justin<div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Could you give some advice? Thanks.<br>
<br>
Best,<br>
<br>
Qin<br>
<br>
</blockquote>
<br></div>
-- <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>
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