<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Nov 11, 2008, at 15:39 , Berk Hess wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">> With Gromacs 4.0 I get this message:<br>><span class="Apple-converted-space"> </span><br>> NOTE: The simulation uses pressure coupling and/or stochastic dynamics.<br>> tpbconv can not provide binary identical continuation.<br>> If you want that, supply a checkpoint file to mdrun<br>><span class="Apple-converted-space"> </span><br>> Is it possible to extend a trajectory with mdrun, a checkpoint file<span class="Apple-converted-space"> </span><br>> and a new tpr-file? E.g:<br>><span class="Apple-converted-space"> </span><br>> tpbconv -s original.tpr -f original.trr -e original.edr -o<span class="Apple-converted-space"> </span><br>> extension.tpr -extend 10000<br>> mdrun -s extension.tpr -cpi original.cpt<br><br>Simply do not supply the trr and edr to tpbconv.<br>mdrun does not read the state from the tpr file, but from the checkpoint file<br>when you give the -cpi option to mdrun.</div></span></blockquote><div><br></div><div>But my example above would also be valid, or? That is, mdrun would take the state from the checkpoint file and the ".mdp-parameters" (tinit, nsteps, etc.) from the .tpr-file?</div><div><br></div><div>Is this the best way to perform a continuation/extension of a simulation?</div><div><br></div><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">> Wouldn't it be nice if one could feed tpbconv with a checkpoint file<span class="Apple-converted-space"> </span><br>> to generate a tpr file?<br><br>Yes, but then the tpr file should contain the whole state.<br>You now never need to create a new tpr file,<br>unless you want to make the run longer than you orginally thought.</div></span></blockquote><div><br></div><div><div>Perhaps it would be more intuative if tpbconv could take a checkpoint file as input and generate a new .cpi-file as starting point for mdrun? Or extend the tpr file format so that it can also include system stat variables.</div><div><br></div><div>Also, why does mdrun override the naming flags for files when using a checkpoint file to start? It always adds ".part000X" before the file extension.</div><div><br></div></div></div></body></html>