[gmx-users] Re,i don't know how can i determine emtol
ivan.gladich at marge.uochb.cas.cz
Wed Nov 21 09:43:17 CET 2012
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
>> 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 :
> 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
> 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.
Ivan Gladich, Ph.D.
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
e-mail: ivan.gladich at uochb.cas.cz
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