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On 12/21/2011 12:57 AM, Thomas Evangelidis wrote:
<blockquote
cite="mid:CAACvdx2Qb3z8LN9xab26JyT80LMQ1bsaHYQ4P9MY3TX-Cc4XqQ@mail.gmail.com"
type="cite">Mark, thanks for the prompt response!<br>
<br>
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<div>I have done Normal Mode Analysis and have calculated
partial charges and the optimized geometry of a few
compounds using high-level QM calculations. Now I want
to see (if possible) how well GROMACS can reproduce the
normal modes if I start from the same optimized geometry
and use the same partial charges.</div>
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<div>In general for NMA to make sense you need to be at a
stationary point w.r.t. the atomic degrees of freedom of the
model being used. That won't be quite true at a QM geometry,
so there's a sense of apples-vs-oranges comparison.</div>
<div class="im">
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<div>If I get it right you mean that NMA in GROMACS must start
from an energy minimum (stationary point) w.r.t the ff used
(GAFF in my case), which means that an energy minimization is
neccessary ever if I use an QM optimum geometry and the
respective partial charges. Namely there is no way to
reproduce the normal modes I obtained from QM calculations,
correct?<br>
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<br>
You can choose to compare the two models on the same configuration,
or at the local minimum w.r.t. each model that is nearest some
configuration. Each approach has a minor flaw. How you need to
manage precision varies with the choice you make.<br>
<br>
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cite="mid:CAACvdx2Qb3z8LN9xab26JyT80LMQ1bsaHYQ4P9MY3TX-Cc4XqQ@mail.gmail.com"
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An obvious problem is that the starting compound geometry
is not in full precision</div>
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<div>The starting geometry is in full precision if it's the
same as that used for the QM calculation. That is quite
possible to achieve with .pdb or .gro input.</div>
<div class="im">
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<div>The same as the starting geometry or as the optimized
geometry?<br>
</div>
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<br>
Your choice - your original workflow did no EM in GROMACS, so the
use of .trr format was immaterial.<br>
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cite="mid:CAACvdx2Qb3z8LN9xab26JyT80LMQ1bsaHYQ4P9MY3TX-Cc4XqQ@mail.gmail.com"
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<div> as highlighted in the documentation:<br>
<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis</a><br>
<br>
Is it possible to create a full precision .trr
coordinate file from a .gro or any other structure file
with modified 8-decimal point coordinates?</div>
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<div>I think you are misunderstanding the use of the word
"precision" here. In general, the same configuration will be
represented differently in .trr and .gro formats, with the
former being a closer approximation. Accordingly, one will
get a different result for NMA on the endpoint of GROMACS EM
as observed in the .trr file and as observed in the .gro
file. The former will be closer to the stationary point, and
so lead to more acceptable estimates of the normal modes.
However, here you want to do NMA on the same coordinates
with two programs, so it is up to you to represent the
coordinates in a way that the two programs can compute on
the same approximation to the coordinates of the stationary
point. There's no need to convert to .trr (or the QM binary
format), because all that does is treat 2.613 as 2.6130000.</div>
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<div><br>
So a command line like this will do the job, right?<br>
<br>
grompp_d4.5.5 -f nm.mdp -c ${ligand}_8_decimal_points.gro -p
${ligand}.top -o nm.tpr<br>
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<br>
That copies the configuration in -c in the full precision available
from the format of -c into the .tpr.<br>
<br>
Mark <br>
<br />--
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