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thanks mark. i guess it took some time answering all these
questions. and i think you are right. trying to interpret each
computed energy term seperately in a physical manner is senseless.
especially since i'm not really deep inside the force field &
implementation stuff. however, with one of your statements i cannot
agree at all: <br>
<br>
imho, free energy diff's on the basis of two conformations and their
steady state distribution are independent from both the energy and
type of the intermediate state. it's only the conversion's rate that
does depend on it. <br>
<br>
but the reason, why i refrained from extracting the potential energy
for a subset of my system was simply due to the difficulties to find
"detailed information" about how to play it out although many
gromacs users have been asking for the issue over the last years. i
needed nearly one full day to figure it out even though it's a
simple series of about 4 gromacs commands only, given some md input
& result files like md.xtc, md.gro, complex.top, index.ndx:<br>
<br>
<code class="java plain">grompp -f mdSubset.mdp -c md.gro -p
complex.top -o mdSubsetTemp.tpr</code><br>
<div class="container" title="Hint: double-click to select code">
<div class="line number1 index0 alt2"><code class="java plain">echo
</code><code class="java string">"1"</code> <code class="java
plain">| tpbconv -s mdSubsetTemp.tpr -nsteps </code><code
class="java value">0</code> <code class="java plain">-n
index.ndx -o mdSubset.tpr</code></div>
</div>
<div class="container" title="Hint: double-click to select code">
<div class="line number1 index0 alt2"><code class="java plain">echo
</code><code class="java string">"1"</code> <code class="java
plain">| trjconv -s mdSubset.tpr -f md.xtc -o mdSubset.xtc</code></div>
</div>
<code class="java plain">mdrun -s mdSubset.tpr -rerun mdSubset.xtc
-v -deffnm mdSubset</code><br>
<br>
where "1" stands for the group to be extracted (from the list of
groups in the index file) and "-nsteps 0" causes recomputation of
for the extracted subset at the given time steps only. i mention it
here so that other users looking for the details might find them a
little bit faster ... it's especially this kind of "tiny tutorials"
that i miss e. g. on the gromacs website.<br>
<br>
thanks for listening and kind regards,<br>
<br>
vedat<br>
<br>
<br>
<blockquote cite="mid:4E9D9C57.4040104@anu.edu.au" type="cite">
<br>
<blockquote type="cite">
<br>
Q8 does anyone have an idea, how to perform the simulation and
on which energy terms to concentrate in order to get reliable
results?
<br>
</blockquote>
<br>
You seem to be performing it OK, given that you've said very
little about any details...
<br>
<br>
I think the problem is poorly constructed. You have some
experimental data that gives a general understanding of the size
of the free energy difference between the isomers. You can't
necessarily expect to reproduce that from (average) potential
energy differences between conformations of those isomers.
Measuring the free energy difference with simulations is hard
because you cannot model the intermediate stages of bond breaking
and forming. There are "alchemical" free energy methods that could
in principle treat this problem effectively, but there will be
some significant issues and you are best doing your own homework
there.
<br>
<br>
Mark
<br>
</blockquote>
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