On Tue, Feb 9, 2016 at 6:56 AM, Thomas Collier <t.collier.12.ucl.ac.uk>
wrote:
> Dear All,
>
> I am currently trying to derive force constants for a new residue in
> amber. I have derived my force constants, but they are significantly
> different to analogous atom types already present in amber. However if I
> do not mass weight the Hessian, the values obtained are close to those
> present for analogous atom types in the parm13.dat file.
>
> My question is are the values for the force constants present in Amber
> parm**.dat files derived from the mass weighted Hessian? Or is the
> atomic mass taken into account later, when running LeaP?
>
I believe it is taken from the mass-weighted Hessian (isn't that the only
way the units work out correctly?). Did you account for the fact that
Amber "force constants" are not really force constants, but rather
half-force constants? That is, the m-w Hessian should give you k such that
U=1/2*k*(x-xeq)^2, whereas the force constants in the Amber parameter files
correspond to U=k*(x-xeq)^2. So they should be half as large (give or
take) as the values you derive from QM frequency calculations.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 09 2016 - 05:00:04 PST
