AMBER Archive (2004)

Subject: Re: AMBER: About the Amber constraint constant

From: Yuhui Cheng (amberuser3_at_yahoo.com)
Date: Tue Aug 17 2004 - 01:34:24 CDT

Hi, Dave,
     I think that you might misunderstand me. In
"_disnrg.f", the comments line is correct, as you
wrote down:
     
     ! r1 <= r <= r2 : E = k2*(r-r2)**2
     ! r2 <= r <= r3 : E = 0
     ! r3 <= r <= r4 : E = k3*(r-r3)**2

     But can you check the program line?
      .....
      else if (rij < r2) then
         dif = rij - r2
         df = 2.0d0 * k2 * dif
         e = k2*dif*dif
      else if (rij <= r3) then
         e = 0.0d0
         do m=1,6
            dfr(m) = 0.0d0
         end do
         return
      else if (rij < r4) then
         dif = rij - r3
         df = 2.0d0 * k3 * dif
         e = k3*dif*dif
      ......

      Subroutine "disnrg" has been used in "nmrred.f
", k2 is the "rk2" and k3 is the "rk3", so in the
program line it seems you didn't think about "1/2",
and I'm not sure whether my understanding is correct.

Thanks,
Yuhui
      
--- "David A. Case" <case_at_scripps.edu> wrote:

> 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
>
>
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