Hello gmx users,
After running energy minimization steps, I got the following error:
teepest Descents:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 100
Step= 0, Dmax= 1.0e-02 nm, Epot= -2.84750e+04 Fmax= 1.53401e+04,
atom= 2501
Step= 1, Dmax= 1.0e-02 nm, Epot= -3.17123e+04 Fmax= 7.71044e+03,
atom= 2501
Step= 2, Dmax= 1.2e-02 nm, Epot= -3.49418e+04 Fmax= 3.42505e+03,
atom= 2822
Step= 3, Dmax= 1.4e-02 nm, Epot= -3.82660e+04 Fmax= 1.91814e+03,
atom= 2822
Step= 4, Dmax= 1.7e-02 nm, Epot= -4.10025e+04 Fmax= 1.19099e+03,
atom= 2300
Step= 5, Dmax= 2.1e-02 nm, Epot= -4.34223e+04 Fmax= 7.57338e+02,
atom= 2300
Step= 6, Dmax= 2.5e-02 nm, Epot= -4.56573e+04 Fmax= 9.04904e+02,
atom= 470
Step= 7, Dmax= 3.0e-02 nm, Epot= -4.68373e+04 Fmax= 1.87844e+03,
atom= 470
Step= 8, Dmax= 3.6e-02 nm, Epot= -4.73705e+04 Fmax= 8.91642e+02,
atom= 470
t = 0.009 ps: Water molecule starting at atom 470 can not be settled.
Check for bad contacts and/or reduce the timestep.
Back Off! I just backed up step9b.pdb to ./#step9b.pdb.1#
Back Off! I just backed up step9c.pdb to ./#step9c.pdb.1#
Wrote pdb files with previous and current coordinates
Step= 10, Dmax= 2.1e-02 nm, Epot= -4.79050e+04 Fmax= 9.54474e+02,
atom= 140
Step= 11, Dmax= 2.6e-02 nm, Epot= -4.83740e+04 Fmax= 1.13333e+03, atom= 14
Step= 12, Dmax= 3.1e-02 nm, Epot= -4.87475e+04 Fmax= 1.27989e+03, atom= 14
Step= 13, Dmax= 3.7e-02 nm, Epot= -4.90791e+04 Fmax= 1.53201e+03,
atom= 500
Step= 14, Dmax= 4.5e-02 nm, Epot= -4.92883e+04 Fmax= 2.07694e+03,
atom= 500
t = 0.015 ps: Water molecule starting at atom 500 can not be settled.
Check for bad contacts and/or reduce the timestep.
Back Off! I just backed up step15b.pdb to ./#step15b.pdb.1#
Back Off! I just backed up step15c.pdb to ./#step15c.pdb.1#
Wrote pdb files with previous and current coordinates
Step= 15, Dmax= 5.3e-02 nm, Epot= -4.94818e+04 Fmax= 3.28279e+06,
atom= 500
Step= 31, Dmax= 2.0e-06 nm, Epot= -4.93789e+04 Fmax= 6.50838e+03,
atom= 500
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Back Off! I just backed up confout.gro to ./#confout.gro.3#
Steepest Descents converged to machine precision in 32 steps,
but did not reach the requested Fmax < 1.
Potential Energy = -4.9481789e+04
Maximum force = 3.2827865e+06 on atom 500
Norm of force = 6.9951227e+04
so I added define = -DFLEXIBLE to my minim.mdp file and the
minimization step ran smoothly. If you are having problems and getting
bad contacts, try adding -Dflexible and hopefully it work fine.
Thanks Chris for your help.
Nisha P
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