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

Ali Alizadeh ali.alizadehmojarad at gmail.com
Wed Nov 21 07:47:48 CET 2012

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 :
>   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

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.



Ali Alizadeh

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