[gmx-users] Energy minimization

Markus O Kaukonen mokaukon at cc.helsinki.fi
Thu Jan 13 11:03:47 CET 2005

Dear All,

My understanding is that Gromacs with constraints does not work with
conjugate gradient minimisation.

To my opinion:
on the other hand one needs constrain water molecules (SPCwater, oplsFF)
(ie bond angle and bond length) in order to
get correct charging energies (and solvation energies)
of ions in a water box. I made this conclusion after some
testing and comparing to literature values

So with systems involving water solvent one should use
constrained water, steepest descent and simulated annealing.
To my experiense the error increases with increasing system size when not
constraining water molecules.

Please correct me if I'm wrong. My test calculation were only qualitive
with energy only (not free energy).

Cheers, Markus

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