Re: [AMBER] iwrap=1 or netcdf

From: Jio M <>
Date: Wed, 15 Jan 2014 08:28:49 -0800 (PST)

Dear Marek

what value of nscm flag you use for trajectories for diffusion analysis? just for curiousity did you observe any difference ?


On Wednesday, January 15, 2014 4:12 PM, Jason Swails <> wrote:
On Tue, Jan 14, 2014 at 11:35 AM, Marek Maly <> wrote:

> Hello,
> regarding simulations for the diffusion study should one
> care about the
> nscm flag ( Flag for the removal of translational and rotational
> center-of-mass (COM) motion ) ?
> ---------------------------------------------------------------------------------------
> "...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. ...."
> "...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. ..."
> -----------------------------------------------------------------------------------------
> If I understand well this flag is here e.g. to compensate perhaps very
> small (especially for bigger systems) but nonzero translational velocity
> of the center of mass of the simulation box content as the result of the
> random assigning of the initial atom velocities. Am I right ?

As I understand it, the flag was originally introduced to solve the 'flying
block of ice' effect introduced by the Berendsen thermostat on explicitly
solvated systems (it would basically convert internal vibrational energy
into rapid translational energy as a consequence of the algorithm itself).

It does serve the purpose you describe as well, but stochastic thermostats
should not have this problem since the _average_ translational momenta will
be zero.  Even if translational momentum is not exactly zero after each
random 'hit', the average over a long trajectory will be zero.  It's also
unnecessary for NVE simulations (that display good energy conservation),
since the law of conservation of momentum holds for Newtonian dynamics.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jan 15 2014 - 08:30:12 PST
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