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

Ivan Gladich ivan.gladich at marge.uochb.cas.cz
Wed Nov 21 09:43:17 CET 2012

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 
It's depends from the initial condition and it requires very long 
Indeed, if I remember well this paper, they observed homogeneous ice 
crystal formation in only one of their trajectories...read carefully the 


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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