AMBER Archive (2006)

Subject: Re: AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion

From: David A. Case (case_at_scripps.edu)
Date: Wed Nov 08 2006 - 10:35:24 CST

On Wed, Nov 08, 2006, Rajesh Murarka wrote:
>
> I have a quick question pertaining to the flag (NSCM) for the removal of
> translational and rotational center-of-mass (COM) motion. I'm doing the
> Langevin dynamics simulations (with GB/SA) of a peptide.
>
> As for this case NTB =0, the default value of NSCM=1000. However, to my
> knowledge, for the Langevin dynamics simulations, the translational COM
> should not remain constant and the rotational COM should fluctuate about
> zero. And I'm not sure what value should I use for NSCM?

For Langevin dynamics, the *position* of the center-of-mass of the molecule is
reset to zero every NSCM steps, but the velocities are not affected. Hence
there is no change to either the translation or rotational components of the
momenta. Doing anything else would destroy the way in which temperature is
regulated in a Langevin dynamics system.

The only reason to even reset the coordinates is to prevent the molecule from
diffusing so far away from the origin that its coordinates overflow the format
used in restart or trajectory files. So you can decide for yourself whether
you need or want to set NSCM to a non-zero value.

Thanks for pointing this out: the code is doing the correct thing, but it is
not documented in the Users' Manual. I will post an erratum to the manual to
correctly explain this.

...regards...dac

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