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*(rintr2). 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*(rintr2)
endif
! calculates the jar force and work (roit. 02/27/05)
fcurr = 2.0*rk2*(rintr2)
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
20090407
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