Dear gromacs users:
I have an issue when I calculate the viscosity with NEMD.
Why the value of 1/viscosity obtained by g_energy in GROMACS remains zero when calculating viscosity with NEMD?
The mdp file is below:
title = production-run
cpp = /lib/cpp
define =
constraints =
integrator = md
dt = 0.001 ; ps !
nsteps = 80000
nstcomm = 1
nstxout = 100
nstvout = 100
nstxtcout = 5000
nstfout = 0
nstlog = 10000
nstenergy = 100
nstlist = 1
ns_type = grid
; Periodic boundary conditions: xyz or no =
pbc = xyz
rlist = 1.3
rcoulomb = 1.3
rvdw = 1.3; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = PME
; Method for doing Van der Waals =
;;;;;;;;;;;;;vdw-type = Switch
; cut-off lengths =
;;;;;;;;;;;;;;;;rvdw-switch = 1.3
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = EnerPres
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.08
; 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-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; Nose-Hoover temperature coupling is on
Tcoupl = berendsen
tc-grps = PF6 c10
tau_t = 0.05 0.05
ref_t = 300.00 300.00
; Energy monitoring
energygrps = PF6 c10
; Pressure coupling is on
Pcoupl = no
tau_p = 1.0
;Non-equlibrium MD
cos_acceleration = 0.06
; Generate velocites is on at 300 K.gen_vel = no
gen_temp = 300.00
gen_seed = 273529
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