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

[Ali Alizadeh]

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


-- 
Sincerely

Ali Alizadeh