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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