[gmx-users] Helpful Information Energy Minimization errors

[nishap.patel at utoronto.ca]

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