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

[Mark Abraham]

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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