[gmx-users] Error:EM did not converge while using polarizable ion
折晓会
shexh19 at hotmail.com
Sun Aug 2 00:38:49 CEST 2015
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 cubic. The drude particle and its core atom are placed at the same position.
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
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:
; Run parameters
integrator = md
nsteps = 50000
dt = 0.002
; Shell molecular dynamics
emtol = 1
niter = 100
; Output control
nstxout = 500
nstvout = 500
nstcalcenergy = 1
nstenergy = 500
nstlog = 500
; Bond parameters
continuation = no
constraints = none
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid
nstlist = 20
pbc = xyz
; VDW
vdwtype = cut-off
vdw-modifier = Potential-shift
rvdw = 0.8
DispCorr = EnerPres
; Electrostatics
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb = 0.8
pme_order = 4
fourierspacing = 0.8
; Temperature coupling is on
tcoupl = nose-hoover
nh-chain-length = 1
tc-grps = Water non-Water
tau_t = 0.8 0.8
ref_t = 300 300
; Pressure coupling is off
pcoupl = no
; Velocity generation
gen_vel = yes
gen_temp = 300
gen_seed = -1
Best wishes,
Xiaohui
> Date: Fri, 31 Jul 2015 19:57:20 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error:EM did not converge while using polarizable ion
>
>
>
> On 7/31/15 7:15 PM, 折晓会 wrote:
> > Dear all,
> >
> > I am now trying to simulation polarizable LiCl solutions with Gromacs 5.0.5, where SWM4-NDP water model and corresponding polarizable ion model are used. The force field files come from professor Spoel and can be found in the website http://virtualchemistry.org/pol.php.
> >
> > During the simulation, error occurs:
> >
> > step 63: EM did not converge in 100 iterations, RMS force 159.892
> > step 64: EM did not converge in 100 iterations, RMS force 542.311
> > step 65: EM did not converge in 100 iterations, RMS force 1064.542
> > step 66: EM did not converge in 100 iterations, RMS force 1168.229
> > step 67: EM did not converge in 100 iterations, RMS force 853.824
> > step 68: EM did not converge in 100 iterations, RMS force 842.719
> > step 69: EM did not converge in 100 iterations, RMS force 1211.043
> > step 70: EM did not converge in 100 iterations, RMS force 2015.682
> > step 71: EM did not converge in 100 iterations, RMS force 2926.036
> > step 72: EM did not converge in 100 iterations, RMS force 3314.541
> > step 73: EM did not converge in 100 iterations, RMS force 4813.701
> > step 74: EM did not converge in 100 iterations, RMS force 9258.925
> > step 76: EM did not converge in 100 iterations, RMS force 1761.227
> > step 77: EM did not converge in 100 iterations, RMS force 589.506
> > Segmentation fault (core dumped)
> >
> > I also try to simulate the pure water with SWM4-NDP model, and it works well. I am wondering if anyone can help me. I failed to find answers on Google and am stuck here for a long time.
> >
> > The force field for ions are as follows:
> >
> > ; Lithium, Li+
> > [ moleculetype ]
> > ; molname nrexcl
> > Li 1
> >
> > [ atoms ]
> > ; id at type res nr residu name at name cg nr charge
> > 1 Lic 1 Li Lic1 1 1.3104270
> > 2 Lis 1 Li Lis1 1 -0.3104270
> >
> > [ polarization ]
> > ; See notes above. alpha (nm^3)
> > 1 2 1 0.000032
> >
> >
> > ; Chloride, Cl-
> > [ moleculetype ]
> > ; molname nrexcl
> > Cl 1
> >
> > [ atoms ]
> > ; id at type res nr residu name at name cg nr charge
> > 1 Clc 1 Cl Clc1 1 2.4571870
> > 2 Cls 1 Cl Cls1 1 -3.4571870
> >
> > [ polarization ]
> > ; See notes above. alpha (nm^3)
> > 1 2 1 0.003969
> >
> >
> > Any help will be appreciated!
> >
>
> Can you provide the contents of your .mdp file? What was the outcome of energy
> minimization prior to starting this run?
>
> -Justin
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.o
More information about the gromacs.org_gmx-users
mailing list