Dear David and all,<br>
<br>
Please see this earlier thread from Michael Shirts:
<a href="http://www.gromacs.org/pipermail/gmx-users/2003-December/008429.html">http://www.gromacs.org/pipermail/gmx-users/2003-December/008429.html</a>. I
think the problem we're seeing is the same one he reported there. It's
possible there are other issues as well, as in our case we're not using
pressure regulation so the box size shouldn't be changing. <br>
<br>
Thanks,<br>
David<br><br><div><span class="gmail_quote">On 10/25/05, <b class="gmail_sendername">David Mobley</b> <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</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;">
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><span class="sg">
David</span><div><span class="e" id="q_10728688971250c4_2"><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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
spoel@xray.bmc.uu.se
</a> <a href="mailto:spoel@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">spoel@gromacs.org</a> <a href="http://xray.bmc.uu.se/%7Espoel" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://xray.bmc.uu.se/~spoel</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br><br>
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