[gmx-users] Energy Minimization Error
jalemkul at vt.edu
Fri Oct 20 02:23:05 CEST 2017
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.
> 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=
>>> Step= 1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, atom=
>>> Step= 2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, atom=
>>> Step= 3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom=
>>> Step= 4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom=
>>> Step= 5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom=
>>> Step= 6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom=
>>> Step= 7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom=
>>> Step= 8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom=
>>> Step= 9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom=
>>> Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom=
>>> 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
>>> ; 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
>>> ; 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 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
>> Gromacs Users mailing list
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users