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 -- 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-requ...@gromacs.org.