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On 20/10/2011 7:25 PM, Vedat Durmaz wrote:
<blockquote cite="mid:4E9FDB12.4010207@zib.de" type="cite">
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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>
</blockquote>
<br>
I'm not sure with which statement of mine you are disagreeing. The
free energy is a state function, and so the free energy difference
between E and Z isomers does not depend on the path taken for the
conversion. The difficulty is just that there is no path for a
cyclic alkane from E to Z in a normal MD force field.<br>
<br>
<blockquote cite="mid:4E9FDB12.4010207@zib.de" type="cite"> <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>
</blockquote>
<br>
There's an art to trying to find detailed help. I know I've given
the advice to make subsets and use mdrun -rerun several times, but I
don't know how a newcomer is ever going to figure that out on their
own!<br>
<br>
BTW -nsteps 0 is not necessary. mdrun -rerun only computes on the
frames present in the input trajectory file. Also, if the index
group of interest is already present in the .tpr that ran the
simulation, then you can do the job with variations on only the
latter three commands.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:4E9FDB12.4010207@zib.de" type="cite"> <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>
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