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AMBER Archive (2008)Subject: AMBER: removing COM and rotation in explicit solvation
From: Naser Alijabbari (na3m_at_virginia.edu)
Hello,
These are my simulation steps: 18 ps NVT to reach 300K, 100 ps NPT to reach
Are there any way/s of removing both translation and rotation (i.e.
if( ifbox == 0 ) then
! ---Non-periodic simulation: remove both translation and
! Back the coords up 1/2 step, so that the correspond to the
! velocities; temporarily store in the F() array:
f(1:nr3) = x(1:nr3) - v(1:nr3)*dt5
! --- now compute the com motion, remove it, and recompute
) before the start of production run w/o using implicit solvations/GB model?
I use Langevin for equilibration phase and I came across this discussion by
"…molecule experiences small but identical COM trans/rot energies between
"Therefore, it seems to me that something is either wrong with the
"These identical "random" forces at every restart seem to affect the net
So I wanted to remove this translation and rotation before the production
Thanks
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