Mo,
I believe this depends on which module you use. This is from memory, but I
think nmropt uses the first form while ncsu_pmd uses the second.
I would say you should check this by hand, but the ncsu modules don't seem
to print any restraint energy to mdout, nor do they make any additions to
the potential energy. I've actually never noticed that before since I
usually just use the coordinate output to recompute the bias energy.
I don't have a ready sample input for nmropt, otherwise I would post some
single point energy results.
Regards,
Brian
On Thu, Apr 19, 2012 at 1:46 PM, Mo Chen <mc842.cornell.edu> wrote:
> Dear Amber developers/users,
> May I ask how is the force constant defined in the biased potential of
> umbrella sampling? Is it the k of
>
> Ubiased=k(r-rc)^2
>
> or
>
> Ubiased = k/2*(r-rc)^2
>
> ?
>
> Thank you!
>
> Best,
> Mo
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>
--
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Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
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Department of Chemistry : Piscataway, NJ
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radakb.biomaps.rutgers.edu
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Received on Thu Apr 19 2012 - 11:30:03 PDT
