[gmx-users] Grompp note
Nilesh Dhumal
ndhumal at andrew.cmu.edu
Thu Oct 31 15:30:50 CET 2013
Hello,
I am running a equilibration simulation for ionic liquids at 400 K.
I am getting following note.
The sum of the two largest charge group radii (0.213127) is larger than
rlist (1.000000) - rvdw (0.900000)
Could you tell what is the problem? I am using Gromacs VERSION 4.5.5 .
I used the following mdp file.
; RUN CONTROL PARAMETERS =
integrator = sd
; start time and timestep in ps =
tinit = 0
dt = 0.001
nsteps = 200000
; number of steps for center of mass motion removal =
nstcomm = 100
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 0
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 5000
nstenergy = 1000
; Output frequency and precision for xtc file =
nstxtcout = 5000
xtc-precision = 1000
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps = system
tau_t = 0.1
ref_t = 400
;OPTIONS FOR PRESSURE COUPLING
Pcoupl = berendsen
tau_p = 0.5
compressibility = 4.5e-05
ref_p = 1.0
; OPTIONS FOR BONDS =
constraints = hbonds
; Type of constraint algorithm =
constraint-algorithm = Lincs
; Do not constrain the start configuration =
unconstrained-start = no
; Relative tolerance of shake =
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order = 12
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle = 30
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = pme
;rcoulomb-switch = 0
rcoulomb = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r = 1
; Method for doing Van der Waals =
vdw-type = switch
; cut-off lengths =
rvdw-switch = 0.8
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = EnerPres
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.1
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters =
pme_order = 6
ewald_rtol = 1e-06
epsilon_surface = 0
optimize_fft = no
; Free energy control stuff
free_energy = no
Nilesh
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