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
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
