[gmx-users] increasing forces during energy minimization
Ingo Appenzeller
ingo.appenzeller at gmx.de
Thu Sep 11 15:55:17 CEST 2014
Dear GROMACS community,
I’ve got some problems getting my energy minimization with mdrun work right for my solution barium-sulfate-ions in water (tip4p). After some steps of calculation (integrator=steep) an decreasing forces, the forces begin to fastly increase again by multiple dimensions. The calculation ist stopped with Epot = –nan. Here the complete output after starting grompp and mdrun:
“Back Off! I just backed up md.log to ./#md.log.11#
Reading file topol.tpr, VERSION 4.6.5 (single precision)
Using 1 MPI thread
Using 2 OpenMP threads
Back Off! I just backed up traj.trr to ./#traj.trr.10#
Back Off! I just backed up ener.edr to ./#ener.edr.10#
Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 50000
Step= 0, Dmax= 1.0e-03 nm, Epot= -1.32579e+05 Fmax= 1.05935e+04, atom= 5893
Step= 1, Dmax= 1.0e-03 nm, Epot= -1.33511e+05 Fmax= 9.70591e+03, atom= 5893
Step= 2, Dmax= 1.2e-03 nm, Epot= -1.34590e+05 Fmax= 8.73726e+03, atom= 5893
Step= 3, Dmax= 1.4e-03 nm, Epot= -1.35838e+05 Fmax= 7.86312e+03, atom= 12489
Step= 4, Dmax= 1.7e-03 nm, Epot= -1.37251e+05 Fmax= 6.97747e+03, atom= 12489
Step= 5, Dmax= 2.1e-03 nm, Epot= -1.38845e+05 Fmax= 6.07222e+03, atom= 13045
Step= 6, Dmax= 2.5e-03 nm, Epot= -1.40644e+05 Fmax= 5.17057e+03, atom= 13045
Step= 7, Dmax= 3.0e-03 nm, Epot= -1.42687e+05 Fmax= 4.29438e+03, atom= 13045
Step= 8, Dmax= 3.6e-03 nm, Epot= -1.45028e+05 Fmax= 3.46452e+03, atom= 13045
Step= 9, Dmax= 4.3e-03 nm, Epot= -1.47752e+05 Fmax= 2.69784e+03, atom= 13045
Step= 10, Dmax= 5.2e-03 nm, Epot= -1.50986e+05 Fmax= 2.12213e+03, atom= 6097
Step= 11, Dmax= 6.2e-03 nm, Epot= -1.54713e+05 Fmax= 1.67687e+03, atom= 6097
Step= 12, Dmax= 7.4e-03 nm, Epot= -1.58896e+05 Fmax= 1.29268e+03, atom= 6097
Step= 13, Dmax= 8.9e-03 nm, Epot= -1.63532e+05 Fmax= 9.75267e+02, atom= 10463
Step= 14, Dmax= 1.1e-02 nm, Epot= -1.68496e+05 Fmax= 9.16984e+02, atom= 11
Step= 15, Dmax= 1.3e-02 nm, Epot= -1.72701e+05 Fmax= 2.03812e+03, atom= 11
Step= 16, Dmax= 1.5e-02 nm, Epot= -1.74483e+05 Fmax= 5.56818e+03, atom= 11
Step= 17, Dmax= 1.8e-02 nm, Epot= -1.75619e+05 Fmax= 2.56424e+04, atom= 15
Step= 18, Dmax= 2.2e-02 nm, Epot= -1.90325e+05 Fmax= 5.23639e+06, atom= 11
Step= 24, Dmax= 8.3e-04 nm, Epot= -2.09743e+05 Fmax= 2.60194e+07, atom= 11
Step= 25, Dmax= 1.0e-03 nm, Epot= -2.48560e+05 Fmax= 1.15010e+08, atom= 15
Step= 33, Dmax= 9.4e-06 nm, Epot= -2.50790e+05 Fmax= 1.22044e+08, atom= 15
Step= 36, Dmax= 2.8e-06 nm, Epot= -2.51480e+05 Fmax= 1.24264e+08, atom= 15
Step= 38, Dmax= 1.7e-06 nm, Epot= -2.51892e+05 Fmax= 1.25597e+08, atom= 15
Step= 40, Dmax= 1.0e-06 nm, Epot= -nan Fmax= 3.38430e+03, atom= 16
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 10 (which may not be possible for your system). It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Back Off! I just backed up outSULWA2min.gro to ./#outSULWA2min.gro.3#
Steepest Descents converged to machine precision in 41 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -2.5189184e+05
Maximum force = 1.2559665e+08 on atom 15
Norm of force = 1.3859668e+06
NOTE: 14 % of the run time was spent in pair search,
you might want to increase nstlist (this has no effect on accuracy)“
Mdrun seems to skip some calculation steps after the 18th step as well.
My commands were as follows:
grompp -f minim.mdp
-c outBASULWA.gro
-p topolSUL1.top
-o topolSULWAmin.tpr
mdrun -v
-c outBASULWAmin.gro
-s topolSULWAmin.tpr
I’d be quite thankful for any hint.
With kind regards
Ingo Appenzeller
Karlsruhe Institute of Technology
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