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

[Thomas Evangelidis]

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. 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 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 am looking forward for an answer,
Thomas
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