Dear Group,
I want to use Amber 9 to do steering molecular dynamics (SMD) simulations with harmonic forces exerted on two ends of a protein.
I would like to implement this as a harmonic constraint, i.e., constraining atoms A and B to destinate positions A' and B', but I also want to have different spring constants in each spatial directions, which mimics pulling in given directions instead of towards fixed points.
After a search in the archive I found that modifying the xconst() subroutine in ene.f could implement different spring constants. And I did the following
do ii = 1,natc
i = igroup(ii)
if(myatm(i))then
#---------- modified ---------------------------
ii3=3*ii-3
wt_x = weit(ii3+1)
wt_y = weit(ii3+2)
wt_z = weit(ii3+3)
#-----------------------------------------------
i3 = 3*i-3
ax = x(i3+1)-xc(i3+1)
ay = x(i3+2)-xc(i3+2)
az = x(i3+3)-xc(i3+3)
#---------- modified ---------------------------
wx = wt_x*ax
wy = wt_y*ay
wz = wt_z*az
#-----------------------------------------------
eadd = wx*ax+wy*ay+wz*az
econ = econ+eadd
f(i3+1) = f(i3+1)-(wx+wx)
f(i3+2) = f(i3+2)-(wy+wy)
f(i3+3) = f(i3+3)-(wz+wz)
endif
end do
Simply put, I want to input a length 3 array of restraint weight instead of a single weight.
Now my question is,in the restraint file, how should I input the the constraints, specificly, how is the restraint constant read into the subroutine? Any hint or suggestion are welcome.
Thanks in advance,
ChengZhong
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Received on Wed Mar 12 2008 - 06:07:35 PDT
