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From: Yuhui Cheng <amberuser3.yahoo.com>

Date: Mon, 16 Aug 2004 23:34:24 -0700 (PDT)

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.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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*> The AMBER Mail Reflector
*

*> To post, send mail to amber.scripps.edu
*

*> To unsubscribe, send "unsubscribe amber" to
*

*> majordomo.scripps.edu
*

*>
*

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Received on Tue Aug 17 2004 - 07:53:02 PDT

Date: Mon, 16 Aug 2004 23:34:24 -0700 (PDT)

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.scripps.edu> wrote:

-----------------------------------------------------------------------

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Received on Tue Aug 17 2004 - 07:53:02 PDT

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