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<br><br>> Date: Sat, 31 Jan 2009 01:30:11 +1100<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] restarting a replica exchange simulations<br>> <br>> sarbani chattopadhyay wrote:<br>> > Hi,<br>> > I had previously ran a replica exchange molecular dynamics <br>> > simulation for 10ns. There<br>> > were 17 ".tpr" input files for 17 replicas at 17 different temperatures.<br>> > However, the run had stopped and now I need to restart it. I <br>> > had generated 17 ".tpr"<br>> > files for the rest of the simulation left, using the command "tpbconv", <br>> > that is usually used for<br>> > generating ".tpr" file to restart a "md" run.<br>> > Then again I gave the command for "mdrun" using "replex" <br>> > option such that the input<br>> > files are the 17 new restart ".tpr " files.<br>> > <br>> > Is this the right way to restart the replica exchange molecular dynamics <br>> > simulation? Will the<br>> > trajectories of the 17 replicas start from the point inteneed and <br>> > perform replica exchange as<br>> > per the command?<br>> <br>> Under 3.x you need to apply a suitable, consistent tpbconv to each <br>> independent simulation - see <br>> http://wiki.gromacs.org/index.php/Doing_Restarts. Under 4.x the restart <br>> mechanism has changed, and the checkpoint file is now the main thing you <br>> have to take care of. I'll update the wiki once I've needed to work out <br>> how that works.<br>> <br>> Mark<br><br>Restarting from checkpoints is trivial for normal simulations.<br>But for REMD simulations there is currently no mechanism that ensures<br>that all replicas write checkpoints at the same step.<br>In 4.0.4 the replace setup will at least allow the checkpoint to<br>be at different steps at long at they are between the same exchange steps.<br>A proper solution will be implemented in 4.1.<br><br>But it seems that under normal conditions checkpoints will usually be written<br>at the same step for all replicas.<br><br>Berk<br><br><br /><hr />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
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