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
--
========================================
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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