AMBER Archive (2009)

Subject: Re: [AMBER] A question about SMD force constant

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Apr 07 2009 - 05:32:09 CDT

if the equation for the energy is k(r-r0)^2, then the force is
2k(r-r0)*(dr/dx). the 2 comes from taking the derivative.

in fact the force constant is actually twice what you input,. the value in
the file is really k/2 since the equation for a harmonic restraint is
usually written as k/2 * (r-r0)^2.
so the force constant k in your case is actually 10 since you input 5 as
k/2.
from the amber manual: "Note that the conventionally defined "force
constant" is twice the value rk2,"

2009/4/6 Jackie. J. Shen <shj.ecust_at_163.com>

> Dear Ambers:
>
> I am puzzled about the restraint constant in the SMD used in amber. I want
> to pull the ligand out from the receptor. So I change the distance between
> one atom in the ligand and one atom in the receptor. the dist.RST is:
>
> ------------------dist.RST------------------------
> &rst
> iat=1291,3973,
> r2=12.09562, rk2=5., r2a=32.09562,
> /
> --------------------------------------------------
> Does it mean that the force constant used here is 5 kcal/(mol*ans) ?
>
> However, I found that in the source code of nmr.f, the force was calculated
> by 2.0*rk2*(rint-r2). I can not understant why the force should be be
> multiplied by 2.0?
>
> What is the exactly force constant used here? 5 or 10 ?
>
> ----------------------nmr.f-----------------------
> ......
> ! Set jar variables to the initial values (roit. 02/27/05)
>
> if(ifirst == 1) then
> work = 0.0
> fold = 2.0*rk2*(rint-r2)
> endif
>
> ! calculates the jar force and work (roit. 02/27/05)
> fcurr = -2.0*rk2*(rint-r2)
> work = work + (fcurr + fold) * drjar/2.0
> fold = fcurr
>
> if (mod(nstep,idmpav) == 0) then
> write(idumpu,'(f12.5,2x)',advance='no') r2*convrt
> write(idumpu,'(f12.5,2x)',advance='no') rint*convrt
> write(idumpu,'(f12.5,2x)',advance='no') fcurr/convrt
> write(idumpu,'(f12.5,2x)',advance='no') work/convrt
> end if
> end if !master
> end if !jar
> ......
> ------------------------------------------------------------------
>
> Thank you very much and best regards!
>
>
> Jackie
> 2009-04-07
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber