On 12/21/2011 12:57 AM, Thomas Evangelidis wrote:
Mark, thanks for the prompt response!
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.
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.
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?
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.
An obvious problem is that the starting compound geometry is not
in full precision
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.
The same as the starting geometry or as the optimized geometry?
Your choice - your original workflow did no EM in GROMACS, so the use of
.trr format was immaterial.
as highlighted in the documentation:
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
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?
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.
So a command line like this will do the job, right?
grompp_d4.5.5 -f nm.mdp -c ${ligand}_8_decimal_points.gro -p
${ligand}.top -o nm.tpr
That copies the configuration in -c in the full precision available from
the format of -c into the .tpr.
Mark
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