[gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges

[Thomas Evangelidis]

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?


> 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?


> 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



Thomas





======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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