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

Ali Alizadeh ali.alizadehmojarad at gmail.com
Thu Nov 22 21:35:49 CET 2012

Dear Ivan

Thank you very very much!

On Thu, Nov 22, 2012 at 2:47 PM, Ivan Gladich
<ivan.gladich at marge.uochb.cas.cz> wrote:
> 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,
> 8641–8653)
>  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.
> http://marge.uochb.cas.cz/~gladich/Teaching.html

That's right,

Is it possible that i know how can you construct it?
You use TIP5P, and i do not know your force field?

In fact i should  construct this structure by self,
Can you give some advices so that i can construct it?

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


Ali Alizadeh


Ali Alizadeh

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