[gmx-users] Energy Minimization Error

[Amali Guruge]

Dear Gromacs Users,

I tried to energy minimize my system using the steep integrator. However,
it gave the following message.

Steepest Descents:
   Tolerance (Fmax)   =  5.00000e+02
   Number of steps    =         2000
Step=    0, Dmax= 1.0e-02 nm, Epot=  3.96157e+06 Fmax= 1.00697e+06, atom=
14611
Step=    1, Dmax= 1.0e-02 nm, Epot=  2.99970e+06 Fmax= 4.04778e+05, atom=
18527
Step=    2, Dmax= 1.2e-02 nm, Epot=  1.54766e+06 Fmax= 1.52387e+05, atom=
1005
Step=    3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom=
6994
Step=    4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom=
58902
Step=    5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom=
515
Step=    6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom=
188631
Step=    7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom=
188631
Step=    8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom=
188631
Step=    9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom=
188631
Step=   10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom=
188631

step 11: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

After 2000 steps it says,

Steepest Descents did not converge to Fmax < 500 in 2001 steps.
Potential Energy  = -4.6310655e+06
Maximum force     =  6.7453154e+03 on atom 18769
Norm of force     =  3.3632809e+01

Simulation ended prematurely, no performance report will be written.


my em.mdp file contains following parameters.

integrator    =  steep            ; simulation algorithm
dt        =  0.002            ; time step (ps)
nsteps        =  2000                ; # steps
comm_mode    =  linear            ; c.o.m. motion reset
;
;    Energy Minimization
emtol        =  500                ; converged F lt value (kJ mol-1 nm-1)
emstep        =  0.01             ; initial step size (nm)
;
;    Output Control
nstxout        =  5                 ; write coordinates to .trr
nstvout        =  5                ; write velocities to .trr
nstlog        =  5                ; write energies to .log
nstenergy    =  1                ; write energies to .edr
;
;    Neightbour Searching
cutoff-scheme   =  Verlet                        ; scheme used for
generating pair list
nstlist         =  10                           ; update neighbour list
ns_type        =  grid                ; neighbour list method
pbc        =  xyz                ; periodic boundary conditions
rlist        =  0.9                 ; cut-off for short-range neighbour (nm)
;
;    Electrostatics and VdW
coulombtype    =  PME                ; type of coulomb interaction
rcoulomb    =  0.9                ; cut-off distance for coulomb
epsilon_r    =  1                ; dielectric constant
rvdw        =  0.9                ; cut-off for vdw
fourierspacing    =  0.12                ; maximum grid spacing for FFT
pme_order    =  4                ; interpolation order for PME
ewald_rtol    =  1e-5                ; relative strength of Ewald-shifted
DispCorr        =  EnerPres                     ; long range dispersion
corrections
;
;    Temperature Coupling
Tcoupl        =  no                ; type of temperature coupling
;
;    Pressure Coupling
Pcoupl        =  no                 ; type of pressure coupling
;
;    Velocity Generation
gen_vel        =  no                 ; generate initial velocities
;
;    Bonds
constraints    =  none                ; bond constraint type

I used gmx solvate to add water molecules to the system.

How could I get rid of bad contacts of water molecules? Appreciate if
anyone help me to solve the problem.

Thank you.

Sincerely,
A Guruge