[gmx-users] Error:EM did not converge while using polarizable ion
jalemkul at vt.edu
Sun Aug 2 01:20:08 CEST 2015
On 8/1/15 6:38 PM, 折晓会 wrote:
> Thank you Professor Justin for your reply!
> The .mdp files for energy minimization and equilibration are shown in the
> following. During the energy minimization, the simulation stops at step=38,
> which may be unreasonable. The initial configuration of the system is simple
Well, what is the maximum force after EM? That tells you whether or not its
reasonable, not the number of steps taken.
> cubic. The drude particle and its core atom are placed at the same position.
Yep, I know how Drude systems are built; I develop the force field :)
> The .mdp file for energy minimization is:
> integrator = steep emtol = 1 niter = 100 emstep =
> 0.01 nsteps = 50000
> nstcalcenergy = 1 constraints = none
> nstlist = 1 cutoff-scheme = Verlet ns_type =
> grid coulombtype = PME rcoulomb = 0.8 rvdw =
> 0.8 pbc = xyz
These cutoffs are much too short.
> The outcome of the energy minimization is:
> Step= 31, Dmax= 2.7e-05 nm, Epot= -2.06027e+07 Fmax= 3.15846e+12, atom=
> 600 Step= 35, Dmax= 4.1e-06 nm, Epot= -1.74228e+08 Fmax= 2.28102e+14, atom=
> 600 Step= 38, Dmax= 1.2e-06 nm, Epot= -9.57138e+07 Fmax= 6.87661e+13, atom=
> 600 Energy minimization has stopped, but the forces have not converged to
> the requested precision Fmax < 1 (which may not be possible for your system).
> It stopped because the algorithm tried to make a new step whose size was too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
> The .mdp file for equilibration is:
Lots of problems here. See annotations below.
> dt = 0.002
dt should never be larger than 0.001 for a polarizable system, *especially* one
with ions. Water is somewhat forgiving; ions and biomolecules are not. This is
probably your biggest problem, but you have lots more.
> ; VDW vdwtype = cut-off
> vdw-modifier = Potential-shift
> rvdw = 0.8
> DispCorr = EnerPres
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2
DispCorr = EnerPres
> ; Electrostatics coulombtype = PME
> coulomb-modifier = Potential-shift-Verlet
> rcoulomb = 0.8
Use rcoulomb = 1.2
> pme_order = 4
> fourierspacing = 0.8
Wildly inappropriate fourierspacing. Your PME will be terribly inaccurate. Use
0.1 or 0.12.
> ; Temperature coupling is on
> tcoupl = nose-hoover
It is unwise to start the simulation with Nose-Hoover in the SCF regime. Try
something more forgiving like V-rescale.
> nh-chain-length = 1
> tc-grps = Water non-Water
Too few degrees of freedom in the ion group to justify its own group. Just
> tau_t = 0.8 0.8
You seem to like 8's :) This may be too weak of coupling. Try 0.5 or 0.1.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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