On 9/15/12 12:49 PM, Elie M wrote:
Dear all,
I have a small question regarding energy minimization. I am minimizing a carbon
naotube in vaccuo and my (mdp )input file is: ;
; SWNT (10,0) on its own
; Elie Moujaes, SWNT+polymers project
; Energy minimization input file
;
cpp =/usr/bin/cpp
define =
-DFLEXIBLE
constraints =
none
integrator =
cg
nsteps =
2000
;
; Energy minimizing stuff
;
emtol = 0.00001
emstep =
0.03
nstcomm =
1
pbc = xyz
periodic_molecules = yes
ns_type =
grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl =
no
Pcoupl =
no
gen_vel =
no
I have put emstep very loww toa chieve accuracy.In the output i got:
Reading file SWNT-EM.tpr, VERSION 4.0.5 (single precision)Polak-Ribiere
Conjugate Gradients: Tolerance (Fmax) = 1.00000e-05 Number of steps =
2000 F-max = 3.48055e+03 on atom 799 F-Norm
= 9.67779e+02
Stepsize too small, or no change in energy.Converged to machine precision,but not
to the requested precision Fmax < 1e-05
Double precision normally gives you higher accuracy.
writing lowest energy coordinates.
Polak-Ribiere Conjugate Gradients converged to machine precision in 359 steps,but
did not reach the requested Fmax < 1e-05.Potential Energy =
8.7646348e+03Maximum force = 1.6186214e+01 on atom 701Norm of force =
5.4860659e+00
It seems that I have to use the double precision version but as the single
precision is concerned,Is the minimization fine (as the maximum force on atom
701 is 16...)?
The outcome seems reasonable. I doubt that any algorithm, in single or double
precision, would ever reach Fmax < 1e-05. Values of Fmax < 10 are generally
suitable for just about any purpose and Fmax < 1000 will generally result in
stable simulations for most systems.
-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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