Re: [AMBER] About force constant in umbrella sampling

From: Brian Radak <>
Date: Thu, 19 Apr 2012 14:11:38 -0400


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.


On Thu, Apr 19, 2012 at 1:46 PM, Mo Chen <> 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
> _______________________________________________
> AMBER mailing list

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Received on Thu Apr 19 2012 - 11:30:03 PDT
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