Dear Phineus,
the lower the better, somewhere between 1-5. Depending on how difficult
the transition from your initial to target conformation is you may need
to increase the force constant, but I'd start with the small values
first. If you need a much bigger force constant (>10 or so) then maybe
targeted md is not the best method for simulating conformational
transition in your system...
Cheers,
-Viktor
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 - 13:53:02 PST
