[gmx-users] Re, problem with EM

Justin Lemkul jalemkul at vt.edu
Tue Nov 20 17:42:13 CET 2012

On 11/20/12 11:30 AM, Ali Alizadeh wrote:
>   Dear All users
>> I want my energy minimization of my system is converged to considered
>> value, when i do it,
>> It is converged because it reachs to Fmax and i see this message :
>> Steepest Descents converged to Fmax < 10 in 31702 steps
>> Potential Energy  = -1.6531438e+03
>> Maximum force     =  9.8014317e+00 on atom 162
>> Norm of force     =  2.9060462e+00
>> my result:
>> http://alichemical.persiangig.com/document/em.jpg
>> When i represent profile of potential energy by g_energy, i can't see
>> my considered results,
>> I should reach this result that this link is related to it,
>> http://alichemical.persiangig.com/document/11.jpg
> Justin wrote:
>           The first plot shows the result of EM, the second is the
> result of a relatively
>          long MD simulation.  I would not expect them to show the same
> result.  Further,
>          it appears that the second plot pertains to the
> configurational energy per water
>         molecule (based on magnitude), while the first simply measures
> the potential
>         energy of the whole system.  Since the system is homogeneous,
> you can use the
>         -nmol option of g_energy to divide the energy terms by the
> number of molecules.
>            -Justin
> 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.

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


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