[gmx-users] why minimization stop so fast
jalemkul at vt.edu
Tue Apr 16 19:09:42 CEST 2013
On 4/16/13 1:05 PM, Albert wrote:
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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