[gmx-users] Re,problem with EM

Justin Lemkul jalemkul at vt.edu
Tue Nov 20 19:06:11 CET 2012

On 11/20/12 1:04 PM, Ali Alizadeh wrote:
> Dear Justin
> Thank you for the quick reply
>> 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
>> 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?
> Justin wrote:
>       If you want to reproduce the results of an MD trajectory, you
> need to be doing
>       MD, not EM.
>       -Justin
> I do not know my emtol value, How can i determine it?

emtol is simply a target value for the maximum force to reach during energy 
minimization.  I don't know that there is a terribly scientific way to determine 
what it should be, except for NMA calculations where it is particularly 
important.  The goal of EM is to achieve a reasonably stable system that is at 
an energy minimum and can be simulated further.



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


More information about the gromacs.org_gmx-users mailing list