AMBER Archive (2009)

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

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Sun May 24 2009 - 15:37:23 CDT

> Dr. Cheatham, if DSUM_TOL and TOL are set to 10^-8 for example, and a 1 step
> MD simulation is used with NSCM=1 with a binary rst file (which doesn't
> exist in AMBER 10), before a production run in NVE with a 1fs integration
> step and ntt=0, do you think one can run a simulation for nanoseconds
> without having the molecule leave the periodic boundary? Or would the energy

In principle, yes. In practice, I haven't tried it.

> somehow couple to an overall translation motion of the molecule no matter
> what? Also what if the molecule crosses main box in PME simulation. Does it
> violate a conservation of angular momentum? I am not sure what "... in the

No, it is fine for the molecule to cross the box and it is natural for
molecules to move and rotate. As far as angular momentum goes, in a
periodic box you cannot remove overall rotation since it is not really
defined.

> case of Langevin, shift the center of mass to zero (or the center of the
> box)" would mean.

With Langevin, you cannot remove translation/rotation since this would no
longer be Langevin; so in this case NSCM simply resets the center of the
molecule to be at the origin. With a periodic system, this doesn't have
meaning since shifting the whole box doesn't matter (and your solute
could still diffuse out)...

--tec3

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