ntxo ! NOT ntx0 :))
Good luck,
M.
Dne Thu, 16 Jan 2014 18:55:20 +0100 Jio M <jiomm.yahoo.com> napsal/-a:
> Hi Marek
>
> Sorry looks like I was sleeping, yes you are right ntx0=2, I dont know I
> misread it somehow and yes thanks for ntwr suggestion
>
> best regards
>
> J
>
>
>
>
> On Thursday, January 16, 2014 5:44 PM, Marek Maly <marek.maly.ujep.cz>
> wrote:
> ntxo=2 should be OK (ntxo=0 is NOT recommended in manual)
>
> see here
>
> http://archive.ambermd.org/201301/0382.html
>
> I am using:
>
> iwrap=0,ioutfm=1,ntxo=2,
>
> without any issues.
>
>
> One more "bonus" tip for you :))
>
> It is a good idea to set explicitly
> ntwr=50000 or to similar number otherwise
> restart file will be by default written
> each 500 steps which will slow down
> your calculation.
>
> Best,
>
> M.
>
>
>
>
>
> Dne Thu, 16 Jan 2014 18:01:23 +0100 Jio M <jiomm.yahoo.com> napsal/-a:
>
>> Hi Marek, Justin, Daniel
>>
>>
>> manual says not recommended.
>>
>> ntx0 = 0 Unformatted (no longer recommended or allowed: please use
>> formatted restart files)
>>
>> I run job in loops so need restart files for every loop
>>
>>
>> What about using, as Daniel suggested, now with iwrap=1,ioutfm=1 then
>> using unwrap with ptraj for analysis?
>>
>> thanks,
>>
>>
>>
>>
>> On Thursday, January 16, 2014 4:52 PM, Marek Maly <marek.maly.ujep.cz>
>> wrote:
>> 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 - 10:30:03 PST
