[gmx-users] Re, problem with EM

Justin Lemkul jalemkul at vt.edu
Tue Nov 20 18:22:29 CET 2012

On 11/20/12 12:17 PM, Ali Alizadeh wrote:
> 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.
>             -Justin
> 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?

If you want to reproduce the results of an MD trajectory, you need to be doing 
MD, not EM.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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