iwrap=0,ioutfm=1,ntxo=2,
is combination you are looking for.
If I am not wrong "ioutfm=1" ensures
NetCDF format just for trajectory files not
for the restart files for which ntxo
flag should be set to value 2.
Best,
M.
Dne Thu, 16 Jan 2014 10:46:20 +0100 Jio M <jiomm.yahoo.com> napsal/-a:
> Hi
>
> 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
> thanks
>
>
>
> On Wednesday, January 15, 2014 5:18 PM, Marek Maly <marek.maly.ujep.cz>
> 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
> comparing
> experimentally measured water self-diffusion with that obtained from the
> simulation using the given water model under the same thermodynamic
> conditions
> as in experiment.
>
> Best wishes,
>
> Marek
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Dne Wed, 15 Jan 2014 17:28:49 +0100 Jio M <jiomm.yahoo.com> 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
>> <jason.swails.gmail.com> wrote:
>> On Tue, Jan 14, 2014 at 11:35 AM, Marek Maly <marek.maly.ujep.cz> 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 Thu Jan 16 2014 - 09:00:03 PST
