<p>When I use .cpt file with tpbconv, I get the error pasted below. I checked the cpt file with gmxdump and it is not empty and has the same number of atoms.</p>
<p>Reading toplogy and stuff from rex_1.tpr<br>Reading file rex_1.tpr, VERSION 4.5.1 (single precision)<br>NOTE: Reading the state from trajectory is an obsolete feaure of tpbconv.<br> Continuation should be done by loading a checkpoint file with mdrun -cpi<br>
This guarantees that all state variables are transferred.<br> tpbconv is now only useful for increasing nsteps,<br> but even that can often be avoided by using mdrun -maxh<br>Modifying ir->bContinuation to TRUE<br>
READING COORDS, VELS AND BOX FROM TRAJECTORY restart1.cpt...</p>
<p>-------------------------------------------------------<br>Program tpbconv, VERSION 4.5.1<br>Source code file: tpbconv.c, line: 451<br>Fatal error:<br>Number of atoms in Topology (8962) is not the same as in Trajectory (0)<br>
For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br><br></p>
<div class="gmail_quote">On Tue, Feb 1, 2011 at 1:04 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br><br>Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">I am doing a manual replica exchange(generalized hamiltonian rem) after every mdrun. If the replica exchange is successful, then I "exchange checkpoint files". For example, consider the following:<br>
Simulation parameters:....................B1.........B2<br>Replicas(coordinates and velocities):.R1.........R2<br> 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY)<br>1. Mdrun run - 500 steps = 1ps<br>
2. Attempt exchange - NOT SUCCESSFUL<br>3. Exchange implementation: SKIP 4.Continue to next step<br> .....<br>0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY)<br>1. Mdrun run - 500 steps = 1ps<br>2. Attempt exchange - If successful, exchange<br>
3. Exchange Implemented by - exchanging checkpointing files<br>4. Continue to next step<br> 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY)<br>1. Mdrun with exchanged .cpt files -NOW this is where the problem shows..<br>
</div> i) The log, xtc files are not appended when beginning after a step with a successful exchange attempt:/According to Mark's previous mail, this could be a result of mismatch in ensembles. Which means that the .cpt is ignored - implying that the mdrun in B1 DOES NOT start from R2./<br>
<br></blockquote><br>Sounds like a reasonable conclusion.
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Therefore, to make R1 run in B2 and R2 run in B1, do I need to supply .cpt to tpbconv instead of mdrun after a successful exchange step?<br>
<br></blockquote><br></div>Either tpbconv or grompp can do this. Check the resulting .tpr with gmxdump to make sure it's using the proper coordinates, velocities, etc from the .cpt file and you'll have your answer as to whether or not it's working as you want.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">To summarize:<br>APPENDING HAS NOW BECOME A SECONDARY CONCERN, WHAT I AM INTERESTED IN IS A SUCCESSFUL MANUAL REPLICA EXCHANGE RUN AS POINTED OUT ABOVE.<br> I hope my dilemma is clear now.<br> Pooja<br> <br>
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<div class="h5">On Tue, Feb 1, 2011 at 11:42 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br></div></div></blockquote></blockquote></div>