[gmx-users] Energy Minimization Error

[Amali Guruge]

Dear Gromacs users,

Thank you very much for the reply. My concern is "step 11: One or more
water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate". What
should I do to avoid it?

Thank you.

On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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