[gmx-users] Energy Minimization Error

[Justin Lemkul]

On 10/19/17 8:10 PM, Amali Guruge wrote:
> 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.

mdrun stopped after 2000 steps because you told it to. You need to 
minimize further, so increase nsteps (or set it to -1 to let mdrun go as 
long as it needs to without having to guess a number).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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