On 4/16/13 1:05 PM, Albert wrote:
Hello:
I've built a system with CHARMM-GUI, and I am trying to mimize it with
following em.mdp file
title = steepest descent energy minimization
define = -DPOSRES -DPOSRES_LIG
cpp = /usr/bin/cpp
include =
integrator = steep
nsteps = 50000
emtol = 0.01
nstcgsteep = 1000 ;step for cg correction ,the larger the more
accurate
nstxout =
nstvout =
nstlog = 100
nstenergy = 10
nstxtcout = 100
nstlist = 10
ns_type = grid
rcoulomb = 1.4
coulombtype = pme
fourierspacing = 0.12
pme_order = 4
rvdw = 1.4
rlist = 1.4
DispCorr = enerpres
constraints = none ; none,hbonds,all-bonds,h-angles,all-angles
cutoff-scheme =Verlet ; GPU running
constraint_algorithm = Lincs
but it stopped after 15 steps.....
Steepest Descents:
Tolerance (Fmax) = 1.00000e-02
Number of steps = 50000
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 0.01 (whichmay not be possible for your system).
It stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Back Off! I just backed up em.gro to ./#em.gro.1#
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 0.01.
Potential Energy = 3.4943549e+18
Maximum force = inf on atom 23533
Norm of force = inf
NOTE: 22 % of the run time was spent in domain decomposition,
6 % of the run time was spent in pair search,
you might want to increase nstlist (this has no effect on accuracy)
gcq#154: "Rub It Right Accross Your Eyes" (F. Zappa)
Your system has severe atomic overlap. You have infinite force on atom 23533.
-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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