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
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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