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

[Mark Abraham]

On 20/12/11, Thomas Evangelidis  <tevang3 at gmail.com> wrote:
> Dear GROMACS users,
> 
> 
> 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.
 

>  The command lines I use are the following:
> 
> 
> ligand="10058_F4.nw.new_GMX"
> 
> ## do Normal Mode Analysis
> grompp_d4.5.5 -f nm.mdp -c ${ligand}.gro -p ${ligand}.top -o nm.tpr
> mdrun_d4.5.5 -v -deffnm nm
> 
> ## calculate the eigenvectors/values of the Hessian matrix and write the eigenvectors to a trajectory file
> 
> g_nmeig_d4.5.5 -f nm.mtx -s nm.tpr -of -ol -v -m -last 81
> 
> ## plot the vector components and the RMS fluctuation per atom of eigenvectors for all eigenvectors
> echo 0 | g_anaeig_d4.5.5 -v eigenvec.trr -s nm.tpr -eig eigenval.xvg -comp -rmsf -last -1
> 
> 
> ## create a trajectory from the eigenvector 76 (the first 6 are the rotation and translation) to visualize the vibrations in VMD
> g_nmtraj_d4.5.5 -s nm.tpr -v eigenvec.trr -eignr "76" -nframes 10 -amplitude 1 -o
> 
> 
> Most of the resulting normal modes do not coincide with the respective ones calculated through QM. Does the order of the above command lines make sense?
> 
> 
> 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.
 

>  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.


Mark
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