AMBER Archive (2009)

Subject: [AMBER] A question about SMD force constant

From: Jackie. J. Shen (
Date: Mon Apr 06 2009 - 20:40:13 CDT

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:

        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 ?

    ! Set jar variables to the initial values (roit. 02/27/05)
      if(ifirst == 1) then
        work = 0.0
        fold = 2.0*rk2*(rint-r2)
            ! 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!


AMBER mailing list