[gmx-users] a fatal error in step mdrun -v -deffnm em &

Brett brettliu123 at 163.com
Wed Mar 30 14:50:02 CEST 2016

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?



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