On Thu, Nov 30, 2023, Mignolet, Alex via AMBER wrote:
>
>I would like to use MMFF, Monte-Carlo,
>and lock the bond distances, bond angles, and bond dihedral angles in
>both the solvent and solute so that only their location and orientation
>may be changed.
>I was drawn to AMBER as the manual states that it allows
>for restraints on molecules as well as modifying the weights of terms in
>the MMFF optimization, which would enable the type of calculation I had
>in mind. It also states that additional intermolecular parameters can be
>added, such as a polarization term, which would be extremely beneficial in
>my case.
Just to add to what Thomas already said: Amber does not support the Merck
Molecular Force Field; it does not include a Monte Carlo option; and it is
not designed to "lock" the internal coordinates in the way you describe.
Support for polarizable force fields for organic liquids is very primitive.
So, if you want to do exactly what you describe above, Amber would not be a
good choice. If, however, you want to optimize mixed solvents around a
(QM?) solute, and follow that up with final QM optimization and
thermodynamic calculations, Amber might be an excellent option: consider
just running "standard" MD using the GAFF2 force field. Don't worry about
how quickly you are searching phase space: the MM part of this should be way
faster than the QM followup you are proposing.
[Obvious caveat to the above advice: I don't really know much about what you
want to do.]
I'd suggest finding a paper that reports something close to what you want to
do, and see how they approached the problem.
...good luck...dac
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Received on Fri Dec 01 2023 - 08:30:02 PST
