[gmx-users] Torsional potential parametrization
jarvit.frost02 at imperial.ac.uk
Fri Apr 27 20:58:14 CEST 2007
Dear Gromacs users,
I'm interested the parametrisation of a torsional angle between successive monomer units - as briefly described on page 13 of Berk Hess' "Molecular dynamics simulations & Gromacs introduction" slides from the 2007 Gromacs Workshop:
As such, we have completed energy scans of a dimer in 'Gaussian' at a suitable level of theory.
Berk's slide then says to use 'mdrun -rerun with the optimized quantum structures' to get the 'Forcefield' view of the total energies.
At this point I'm unsure of what is suggested:
Do I first do an MD run of a single dimer in vacuum (or very large box with pbc) and then use that trajectory, sampling total energies at the torsional angles which it goes through?
Or do I input coordinates of each Gaussian scan structure individually and somehow position restrain the torsional value, and then do a single-point energy calculation somehow?
It seems that using the 'ffscan' program may be the way forward, but documentation is rather sparse.
Any advice, walkthroughs or literature references thankfully received!
The most relevant prior discussion I found is here:
Jarvist Frost <jmf02 at ic.ac.uk>
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