AMBER Archive (2004)

Subject: Re: AMBER: About the Amber constraint constant

From: David A. Case (case_at_scripps.edu)
Date: Sun Aug 15 2004 - 18:07:11 CDT

On Sun, Aug 15, 2004, Yuhui Cheng wrote:

> When Sander set the harmonic constraint using NMR metnod, Dr. Alan
> Grossfield mentioned in his WHAM program that the constraint energy
> should be "E=k*(x-x0)^2" instead of "E=(1/2)*k*(x-x0)^2". I checked the
> fortran source code "_disnrg.f" in the $AMBERHOME/src/sander/ and found
> that the comments line use the formula "E=(1/2)*k*(x-x0)^2" but the
> program line neglected the "1/2". Is my understanding correct?

I guess I'm missing something here: the comments in disnrg.f look OK to me:

   ! r1 <= r <= r2 : E = k2*(r-r2)**2
   ! r2 <= r <= r3 : E = 0
   ! r3 <= r <= r4 : E = k3*(r-r3)**2

I could not find any comment (at least in versions 7 an 8) that correspond
to what you quoted. If you can identify the bad comment more precisely, we
will get it fixed.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu