[gmx-users] Viscosity measurements

[Mikhail Stukan]

Dear gmx-users,

I am trying to simulate coarse-grained dodecane using MARTINI force field. One of the properties I would like to measure is viscosity. I was trying to do this from NEMD (actually  I am using Langevin stochastic dynamics) and I am facing the problem having negative(!)  value for 1/eta  calculated by g_energy.
Am I missing something very obvious?

I am using 4.5.4 version.

Thank you very much in advance.


My .mpd file looks like:

integrator               = sd
dt                               = 0.005
nsteps                     = 1000000
comm_mode        = Linear
nstcomm                 = 100
nstxout                    = 10000          ; write coords
nstvout                   = 10000          ; write velocities
nstfout                    = 0               ; write forces (Do not write them)
nstxtcout                = 0           ; write coords to xtc-trajectory file
nstlog                       = 2000            ; print to logfile
nstenergy               = 100            ; print energies
xtc_precision          = 1000
xtc-grps                      =
energygrps               = DEC

coulombtype              = Shift
rcoulomb_switch       = 0.0
rcoulomb                    = 1.2
epsilon_r                   = 15
vdw_type                 = Shift
rvdw_switch              = 0.9
rvdw                           = 1.2
DispCorr                  = No

tc-grps                  =   DEC
tau_t                    =   2.0
ref_t                    =   300

cos_acceleration         =  0.1

Pcoupl                   = no

gen_vel                  = no
gen_temp                 = 300
gen_seed                 = 473529



=============================================
Dr Mikhail Stukan
Schlumberger Dhahran Carbonate Research Center,
Dhahran Techno Valley  - KFUPM,
P.O. Box 39011, Dammam / Doha Camp  31942,
Kingdom of Saudi Arabia
Tel: +966 3 331 6182
Fax:+966 3 330 0845
mstukan at slb.com<mailto:mstukan at slb.com>

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