Dear David,<br>
<br>
The specific energies which are different are:<br>
LJ (SR)<br>
Coulomb (SR)<br>
Coulomb recip.<br>
Potential<br>
Total energy<br>
dVpot/dlambda<br>
Pressure<br>
<br>
Again, I can make these nearly match the previous run if I use the
correct .gro file -- but the results I get for these are CLEARLY
dependent on the .gro file used, even though I am using the full
precision trr files including velocities. <br>
<br>
Thanks,<br>
David<br>
<br><br><div><span class="gmail_quote">On 10/25/05, <b class="gmail_sendername">David</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Tue, 2005-10-25 at 06:33 -0700, David Mobley wrote:<br>><br><br>><br>> David,<br>><br>> I'm rerunning with a trr file containing velocities. And the potential<br>> energies are different, as are total energies, etc. Additionally, the
<br>> calculations I'm looking at at the moment are free energy<br>> calculations, so the dv/dlambda values are different as well.<br><br>I don't think the rerun option has ever been tested with free energy, if<br>it works your statistics will be far inferior from the original.
<br><br>But please be more specific. Which energy terms are different?<br><br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br><br>
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