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..<br><br>My setting<br>In the .mdp of the previous simulation, gen_vel was on; <br>I didn't record the velocity by putting nstvout =0; <br>
I used xtcgrp = Protein. <br><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">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></div><div class="h5"><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 class="im"><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>
<br>
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