Re: AMBER: removing COM and rotation in explicit solvation

From: David A. Case <>
Date: Sun, 12 Oct 2008 17:32:54 -0400

On Sun, Oct 12, 2008, Naser Alijabbari wrote:
> "?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."

All users need to take care to avoid using the same random number seed for
repeated restarts when a Langevin thermostat is active (ntt=3). In recent
versions of Amber, you can set ig to -1, which will create a random seed based
on the time of day at the start of the job. In earlier versions (or even in
Amber 10 when you are using groups), you need to make sure to set ig to a
different, non-default, value at each restart.

I *think* this should help with your problem.

...good luck...dac

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Received on Mon Oct 13 2008 - 05:08:43 PDT
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