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
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.
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)
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
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.glad...@uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
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