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/
-----

--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to