[gmx-users] IONs + PME run problem!!

[Mungikar, Amol Arvind (UMR-Student)]

Dear gmx-users,
I am here again with another problem. I was trying to run a model peptide + ions in water. The system is electroneutral. I was trying to do a 2 ns md run. 
md.mdp file:

cpp = /lib/cpp

constraints = all-bonds

integrator = md

dt = 0.002 ; ps !

nsteps = 1000000; total 2 ns.

nstcomm = 1

comm_grps = Protein SOL Na

nstxout = 5000

nstvout = 5000

nstfout = 0

nstlog = 500

nstenergy = 500

nstlist = 500

ns_type = grid

rlist = 1.0

coulombtype = PME

rcoulomb = 1.0

rvdw = 1.0

; nose-hoover temperature coupling is on in two groups

Tcoupl = nose-hoover

tc-grps = Protein SOL Na

tau_t = 0.1 0.1 0.1

ref_t = 300 300 300

; Energy monitoring

energygrps = Protein SOL Na

; Isotropic pressure coupling is now on

Pcoupl = no

Pcoupltype = isotropic

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

; Generate velocites is off at 300 K.

gen_vel = yes

gen_temp = 300.0

gen_seed = 173529

EM output

Steepest Descents converged to 100 in 724 steps

Potential Energy = -3.69708e+04

Maximum force: 9.12667e+01

 
MD run output:
t = 383.000 ps: Water molecule starting at atom 1300 can not be settled.

Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates

Energies (kJ/mol)

Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14

1.10620e+02 5.17073e+01 5.82271e+01 3.68468e+01 1.18949e+03

LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En.

2.35068e+06 -3.19766e+04 -5.70743e+03 2.31444e+06 nan

Total Energy Temperature Pressure (bar)

nan nan nan

Fatal error: ci = -2147483648 should be in 0 .. 124 [FILE nsgrid.c, LINE 210]

It says me to reduce the timestep, I didnt understand this, why? 

Am I doing anything wrong with "md.mdp" file!! or the energy minimization is creating a problem. 

Thank you very much for your help!

Amol A Mungikar