[gmx-users] Re,i don't know how can i determine emtol

Ivan Gladich ivan.gladich at marge.uochb.cas.cz
Thu Nov 22 12:17:50 CET 2012

On 11/21/2012 06:02 PM, Ali Alizadeh wrote:
>>> 1- In your opinion, Can i simulate that system?
>> In my (humble) opinion:
>> 1)Of course you can simulate that system...however  I doubt that, without
>> starting from the exact initial configuration with the exactly same set-up,
>> you can get the same results (i.e. see the nucleation).
>> The onset of ice nucleation is a random process and requires very long
>> simulation (the paper that you posted was analysing micro-second
>> trajectories!!).
>> There is the risk that you could try several different initial
>> configurations at several temperature without getting anything.
>>   However, read carefully that paper, I do not remember all the details.
>> If you are interested in ice crystal growth, I would suggest to start with
>> an initial water/ice system: at temperature below the melting one you will
>> see formation of new ice starting from the initial ice matrix.
> I do not know how  can ice crystal in initial step, i study papers and
> i know ice , crystals formation and dissociation of crystals is very
> difficult,
> and we can use this method(as you said above) for melting or
> freezing(if i say correct)
> My problem is this case, how can i have a crystal in initial step,
You have three options

1) Surfing the web searching for some structure.

2)Try to implement the proton disordering algorithm of Buch et al.,
(V. Buch, P. Sandler and J. Sadlej, J. Phys. Chem. B, 1998, 102,
  which specifies orientations of water molecules such that ice
Ih Bernal–Fowler constraints for each molecule are satisfied.
(J. D. Bernal and R. H. Fowler, J. Chem. Phys., 1933, 1, 515–548)

3) Someone kindly offer you his own structure, e.g.


(PS: This is the structure at O K...you have to heat it to the desired 
Good Luck

>> There are several works in literature on this.
>>> 2- How can i use rigid TIP4P model of water?
>> 2)  I would rather use other water model that have been explicitly tested
>> for Ice
>> (e.g. TIP4P/2005, TIP4P/Ice, TIP5P-Ew, NE6)
> I think that i solved it, thank you,
>> Best
>> Ivan
>>> Sincerely
>>> Ali Alizadeh
>> On 11/21/2012 09:43 AM, Ivan Gladich wrote:
>>> Dear Ali
>>>      the paper that you are citing is using a rigid TIP4P water model
>>> As far as I know, emtol is relevant only for minimization or molecular
>>> dynamics with shell particle or flexible constraints.
>>> Therefore, as Justin told you, the emtol value should be irrelevant.
>>> Concerning this paper, I would like to warn you that h_omogeneous ice
>>> nucleation from bulk water_ with explicit water molecule is very rare
>>> event...
>>> It's depends from the initial condition and it requires very long
>>> simulations.
>>> Indeed, if I remember well this paper, they observed homogeneous ice
>>> crystal formation in only one of their trajectories...read carefully the
>>> paper!
>>> Best
>>> Ivan
> --
> Sincerely
> Ali Alizadeh

Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic

Tel: +420775504164
e-mail: ivan.gladich at uochb.cas.cz
web page:http://www.molecular.cz/~gladich/

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