[gmx-users] Energy Minimization Error
Amali Guruge
amaligg2010 at gmail.com
Fri Oct 20 10:27:51 CEST 2017
Dear Gromacs users,
When I tried to run the equilibration run, it gave several LINCS WARNINGS.
However, that equilibration run is completed by the Gromacs. Do I have to
concern about these warnings or can I ignore those?
Thank you.
Sincerely,
A. Guruge
On Fri, Oct 20, 2017 at 11:22 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>> <https://maps.google.com/?q=pped+after+2000+steps+because+you+told+it&entry=gmail&source=g>
>>> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
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