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

Ivan Gladich ivan.gladich at marge.uochb.cas.cz
Wed Nov 21 14:17:11 CET 2012

On 11/21/2012 11:41 AM, Ali Alizadeh wrote:
> Dear Ivan
> Thank you for your reply,
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..;-)
> 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 
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.
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)

> 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
> On 11/21/2012 07:47 AM, Ali Alizadeh wrote:
>> On 11/20/12 3:38 PM, Ali Alizadeh wrote:
>>   Dear Justin
>> Thank you ,
>> This link is the paper that i want to reproduce its results,
>> Title: Molecular dynamics simulation of
>> the ice nucleation and growth
>> process leading to water freezing
>> http://www.nature.com/nature/journal/v416/n6879/pdf/416409a.pdf
>>> I am using MD instead of steep, and i have a problem, I do not know
>>> value of emtol so that energy of system reaches to -51 kj/mol, i
>>> determine it then run it but it reaches to -30 kj/mol(only for 1ns)
>>> original results :
>>>    http://alichemical.persiangig.com/document/11.jpg
>> Justin wrote:
>> >  The value of emtol is only relevant in EM and has no
>> relationship whatsoever to
>> >  MD.  In fact, this keyword is ignored if an EM algorithm
>> is not chosen as the
>> >integrator.
>> This means  When i use the md-vv integrator, emtol is ignored.
>> >No one can help you if you don't fully describe what
>> you're doing.  That appears
>> >to be a figure from some paper - what's going on?  If it
>> is from a paper, what
>> >were the methods?  How was the plot produced?  Otherwise
>> no one will have any
>>             idea what's going on.  You can't just force a system to
>> adopt some series of
>> >configurations that yield a given potential energy.
>> >Please describe in full what you are doing, and provide
>> answers to all the
>> >questions posed above, or else I'm afraid I'm not going to
>> have anything else
>> >useful to say.
>>          -Justin

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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