Dear All, After steps for pdb2gmx, editconf, solvate, "-f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr", genion, "grompp -f minim.mdp -c target_solv_ions.gro -p topol.top -o em.tpr", I started step "mdrun -v -deffnm em &", but in the "mdrun -v -deffnm em &" step it gave
"Step= 15, Dmax= 1.3e-01 nm, Epot= -4.22195e+07 Fmax= 7.18492e+04, atom= 7837 Step= 16, Dmax= 1.5e-01 nm, Epot= -4.23771e+07 Fmax= 1.46229e+05, atom= 5656 Step= 17, Dmax= 1.8e-01 nm, Epot= -4.24412e+07 Fmax= 7.58589e+05, atom= 5656 Back Off! I just backed up step18b_n8.pdb to ./#step18b_n8.pdb.1# Back Off! I just backed up step18c_n8.pdb to ./#step18c_n8.pdb.1# Wrote pdb files with previous and current coordinates ------------------------------------------------------- Program gmx mdrun, VERSION 5.1.2 Source code file: /home/FANFENGHUI/Desktop/WORK2016_2/GROMACS/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555 Fatal error: step 18: Water molecule starting at atom 964420 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. " My minim.mdp was as following, "; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 500.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.4 ; Short-range electrostatic cut-off rvdw = 1.4 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions" Will you please let me know why the fatal error in step 18 occurred, and how to avid it? Based on "Step= 16, Dmax= 1.5e-01 nm, Epot= -4.23771e+07 Fmax= 1.46229e+05, atom= 5656", does it mean that step only works on atop "5656"? If so, if my system contains 500,000 atoms, how much should be the appropriate value for "nsteps" in the minim.mdp file? Brett -- 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 [email protected].
