Re: [AMBER] iwrap=1 or netcdf

From: Jio M <>
Date: Thu, 16 Jan 2014 01:46:20 -0800 (PST)


Even I used ioutfm=1 for netcdf I got **** in restart and job killed. Is that normal? 
So should I use iwrap=1 also?

P.S. I will come to Marek's point later

On Wednesday, January 15, 2014 5:18 PM, Marek Maly <> wrote:
Hi Jio,

actually I did no diffusion study yet :))

But if you do not set nscm parameter, by default
the COM movement corrections will be done each
1000 steps (see the Amber12 manual).

See my last comments regarding my view (understanding) of that
corrections in the framework of the diffusion studies.

Perhaps much more important is to know that different
water models (TIP3P, TIP4P, SPC ...) have also remarkable differences
comparing to real (experimentally measured) diffusion which is connected
with just limited ability of those models to imitate some real water
parameters here e.g. water viscosity.

So especially if you are going to compare your simulation results
with experiments you should to take this in account.

There will be perhaps some articles available describing (quantifying) this
differences for the given water model.

You can perhaps eventually do your own "calibration" experiments by 
experimentally measured water self-diffusion with that obtained from the
simulation using the given water model under the same thermodynamic 
as in experiment.

  Best wishes,


Dne Wed, 15 Jan 2014 17:28:49 +0100 Jio M <> napsal/-a:

> Dear Marek
> what value of nscm flag you use for trajectories for diffusion analysis? 
> just for curiousity did you observe any difference ?
> thanks
> 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.
> HTH,
> Jason

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