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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Received on Wed Apr 08 2009 - 01:13:59 PDT
