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On 19/11/2010 10:15 PM, Reiner Ribarics wrote:
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<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height:
normal;"><span style="font-size: 12pt;">Dear all, <br>
<br>
I know similar topics have already been discussed, but there
is a question regarding pairwise forces that could not be
resolved by reading the mailing list. <br>
<br>
Our group has already done some rather long simulations and
according to the script files forces are written every 10000
steps and can be accessed via trjconv with -cf option that
assigns each atom a temperature factor. I was wondering if
that is the way gromacs stores the forces in the trajectory
file. Or are the temperature factors calculated from other
(maybe pairwise) forces? <br>
</span></p>
</blockquote>
<br>
A trajectory file of T frames of N atoms containing only forces is
simply T sets of 3*N numbers interleaved with some per-frame header
information. There is no way to decompose anything "after the fact".
g_traj works from those forces.<br>
<br>
<blockquote cite="mid:4CE65C6B.4080507@meduniwien.ac.at" type="cite">
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height:
normal;"><span style="font-size: 12pt;"> I also had a look at
FDA gromacs that is able to write out pairwise forces, but
unfortunately it falls back on the rather slow gromacs
routines and we want to avoid rerunning our simulations if
possible. </span><br>
</p>
</blockquote>
<br>
Anything that computes pairwise forces will necessarily be slow, or
a memory-hog, or both.<br>
<br>
Mark<br>
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