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

Ali Alizadeh ali.alizadehmojarad at gmail.com
Wed Nov 21 18:02:40 CET 2012

Dear Ivan

Thank you for your reply,

>> Dear Ivan

> Dear Ali
> please keep the discussion open to everybody...
> In this way you will be sure that someone else  will read and interact with
> us, correcting me if I say something wrong to you..;-)

I receive your email from your personal email,

>> 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
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,

> 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


Ali Alizadeh

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