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

[Ali Alizadeh]

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?


-- 
Sincerely

Ali Alizadeh