[gmx-users] Energy Minimization Error

[Justin Lemkul]

On 10/19/17 8:21 PM, Amali Guruge wrote:
> 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?

That happens often during minimization, especially the early steps. If 
it doesn't come back up again, it's fine. It should never happen during MD.

-Justin

> 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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-- 
==================================================

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

==================================================