<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Hi Berk,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Thanks for your reply. </DIV><BR><DIV><BLOCKQUOTE type="cite"><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; min-height: 14.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">The box is read, but in several parts of the code there are optimizations</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">for fixed box dimensions (i.e. no pcoupl, no deform).</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">This is indeed a bit tricky, but I don't know if we would want to change<SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">this</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">for the rerun option.</FONT></P></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Maybe the optimizations are not necessary for the rerun option, as energy evaluations usually involve a limited number of frames. I think that the box sizes should really be read from the traj. The present behavior seems dangerous (I almost wasted a week of work figuring it out, and some users might never double check...)</DIV><BR><BLOCKQUOTE type="cite"> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">We do want scaling of velocties, since this influences the kinetic energy,</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">also for reruns.</FONT></P></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I never understood this one. The kinetic energy at step N should depend only on the velocities at time step N. If a frame in the trajectory contains the positions and velocities at time step N as it should, no rescaling is necessary. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>If on the other hand only velocities at step N-1/2 are saved, velocities at step N+1/2 would have to be calculated in order to get accurate kinetic energy at step N. In this case, rescaling indeed needs to take place. But the rescaling will be nonsense if a Nosé-Hoover thermostat is used, since the thermostat momentum is not read from the trajectory. If this is the case, there should be a large warning sign when using -rerun with Nosé-Hoover. A solution would be to output the kinetic energy at time step N-1/2 during the rerun, which is in any case more accurate than the one at step N, and is just as good for statistics.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>See a paper coming soon in JCP:</DIV><DIV style="text-align: justify; text-indent: -22px;"><FONT class="Apple-style-span" face="Times">M. M. A. Cuendet and W. F. van Gunsteren, </FONT><FONT class="Apple-style-span" face="Times"><I>On the calculation of velocity-dependent properties in molecular dynamics simulations using the leap-frog integration algorithm</I></FONT><FONT class="Apple-style-span" face="Times">, J. Chem. Phys. </FONT><FONT class="Apple-style-span" face="Times"><B>(in print)</B></FONT><FONT class="Apple-style-span" face="Times"> (2007).</FONT></DIV><BR><BLOCKQUOTE type="cite"><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">We could consider using nstenergy=1 for rerun, but I think that currently</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">you should already get the energy as often as for the original run, unless</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">you use a trajectory without step numbers (e.g. pdb).</FONT></P></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV><DIV>This is good, but without nstenergy=1 the averages are wrong in md.log and at the end of the run.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Bye,</DIV><DIV>Michel</DIV></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; 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; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; 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; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>==========================================================</DIV><DIV>Michel Cuendet, Ph.D</DIV><DIV>Molecular Modeling Group</DIV><DIV>Swiss Institute of Bioinformatics</DIV><DIV>CH-1015 Lausanne</DIV><DIV>Switzerland</DIV><DIV>==========================================================</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN></SPAN> </DIV><BR></BODY></HTML>