[gmx-users] Re, problem with EM

Ali Alizadeh ali.alizadehmojarad at gmail.com
Tue Nov 20 17:30:14 CET 2012

 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.


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?

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

Ali Alizadeh

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