[gmx-users] Re, problem with EM

Ali Alizadeh ali.alizadehmojarad at gmail.com
Tue Nov 20 18:17:40 CET 2012

Dear Justin

Thank you for your reply,

> 1- In the first plot, unit of y axis is kj/mol, and you said above i
> should use -nmol, i  confused, Why is the unit of y axis kj/mol
> without using -nmol?

         Because that's the energy unit Gromacs always uses.  The
energy given is kJ per
         mole of equivalent systems.  In the second plot shown above,
the magnitude of
         the energy suggests kJ per mole of individual molecules.

I understood,

> 2- I want do EM so that energy of my system reaches to considered
> value, but i never reach it exactly, what's wrong?

          You set an EM tolerance of 10 kJ/(mol-nm), which is a force,
and mdrun achieved
           that.  You can't ask an EM algorithm to produce the same
result as a long-time
           MD run, as is shown above.


That's right, I knew it but in your opinion, How can i get same
result, What's the value of emtol for my system?

Ali Alizadeh

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