I don't know of a "good" value, but I think it is best to consider
the energy involved and what magnitude of fluctuations
you want to get. If you put a restraint of 1.0 kcal/mol/A
then you should get deviations less than 1 angstrom
at room T (where 1/2kT is about 0.3 kcal/mol).
Phineus Markwick wrote:
> Dear AMBERers,
>
> can anyone give me a general rough guess-estimate for the force
> constant for TMD?
> I recognise that this parameter can be optimised, given the type of
> system
> and the problem at hand, but what would be a general ball-park figure
> to start
> with for TMD simulation of a protein in explicit water solvent at 300K?
>
> with best regards,
> Phineus Markwick.
>
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Received on Tue Mar 22 2005 - 14:53:00 PST
