[gmx-users] problem with EM

[Justin Lemkul]

On 11/20/12 1:40 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
>

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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