[gmx-users] IONs + PME run problem!!
Mungikar, Amol Arvind (UMR-Student)
mungikar at umr.edu
Mon Feb 16 22:15:02 CET 2004
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.
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
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
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
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