AMBER Archive (2009)

Subject: Re: [AMBER] nanoseconds of simulation with nscm=0

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Sun May 24 2009 - 13:27:33 CDT

> I am trying to understand where center of mass translation and rotation come
> form during a simulation. I came across the following threads
> http://archive.ambermd.org/200705/0176.html
> http://archive.ambermd.org/200601/0154.html. I have never have a simulation
> start in NVE without any COM. Usually there is always some COM, and if I

By COM I assume you mean center of mass motion (not just center of mass).

> understand the thread correctly this is due to accumulation of error when
> integrating equations of motion. So in a nanosecond simulation the molecule
> would move away until coordinates would be too big to write to file. Have
> others been able to start a simulation without any COM?

No, only the growth in center of mass motion is due to lack of complete
energy conservation (energy drains). The initial center of mass motion in
a simulation is simply due to random temperature generation; it is highly
unlikely if you pick a set of velocities at random to match a particular
temperature distribution that the net-translation (or also rotation in a
non-periodic system) will be exactly zero. This will also be true at
every step in Langevin dynamics since random forces are added (however
since they are random, they should not as easily grow if energy
conservation is reasonable).

The net-translation is likely small, but can grow due to lack of complete
energy conservation. Where do we lose energy? Berendsen pressure
coupling; SHAKE tolerances that are not stringent enough; larger time
steps; PME that is not sufficiently accurate; cutoffs in GB; etc.

You can get rid of initial COM motion only at periodic intervals through
the NSCM variable (although I note that it used to be that it was also
removed when not restarting a run however this behavior has changed). If
you want it removed at the initial step, run 1 step of MD with NSCM=1 and
then use the restrt file (IREST=1) for subsequent MD. Note that due to
finite precision in the formatted restrt file, this could still lead to a
(likely smaller) non-zero COM motion. To avoid that would require binary
restrt's.

Note that keeping NCSM set to some interval is helpful as it will report
energy problems or in the case of Langevin, shift the center of mass to
zero (or the center of the box).

Let me know if this doesn't answer your question sufficiently...

--tec3

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