AMBER Archive (2008)

Subject: AMBER: removing COM and rotation in explicit solvation

From: Naser Alijabbari (
Date: Sun Oct 12 2008 - 15:02:22 CDT


These are my simulation steps: 18 ps NVT to reach 300K, 100 ps NPT to reach
~1g/cm^3, and 100ps NVE simulation "production run" (I am following online
tutorial for explicit water simulation, and the time is short but this is
just a test).

Are there any way/s of removing both translation and rotation (i.e.
returning the molecule to the origin using something like the "center"
command in ptraj and using code similar to the one in runmd.f for removing

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?
ptraj does not create restart files so what are my alternatives?

I use Langevin for equilibration phase and I came across this discussion by Dr. Peter Varnai:

"…molecule experiences small but identical COM trans/rot energies between
different fragments of the trajectory."

"Therefore, it seems to me that something is either wrong with the
writing/reading of the restart file and/or each time sander restarts it
assigns some constant, non-random forces to the system?!"

"These identical "random" forces at every restart seem to affect the net
molecular motion in Langevin simulations in a deterministic way. Since the
random forces can produce overall translation and rotation effect, these
repeating forces create quasi-linear translations, especially after
equilibration when the random forces dominate (?) the total force over the
Newtonian and frictional forces."

So I wanted to remove this translation and rotation before the production
NVE run.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)