AMBER Archive (2009)

Subject: [AMBER] A question about SMD force constant

From: Jackie. J. Shen (shj.ecust_at_163.com)
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:

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

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