Re: [AMBER] iwrap=1 or netcdf

From: Marek Maly <>
Date: Wed, 15 Jan 2014 18:00:38 +0100

Hi Jason,

first of all thanks for your valuable comments !

So also considering this your explanation, the fact
that by default each 1000 steps the positions of all particles
in simulation box are "artificially" little shifted to maintain the
in the one point doesn't negatively affect the eventual study of diffusion
chosen molecules or even doing here good job (in cases where due to the
thermostat type would be without corrections remarkable COM movements)
because if I am studying
diffusion movements of the given particle I take care about it's movement
in the coordinate system connected with the COM of my molecular system.

In another words if I would like to study movements of the fish in the
tub which is actually in the moving car and I am external observer
standing on the road I have to subtract car movements to obtain correct
natural movement of the fish relative to the tub with water.

Am I right ?

    Best wishes,


Dne Wed, 15 Jan 2014 17:12:35 +0100 Jason Swails <>

> 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.
> HTH,
> Jason

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Received on Wed Jan 15 2014 - 09:30:02 PST
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