Dear GROMACS users and developers,
I'm having trouble getting values for my 1/viscosity calculation which obtained from g_energy:
g_energy -f md1_vis.edr -o md1_vis_1perv.xvg
the output:
Statistics over 1000001 steps [ 0.0000 through 2000.0000 ps ], 1 data sets
All statistics are over 100001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
1/Viscosity 0 0
0 0 (m s/kg)
gcq#310: "Shoot them in the back now" (The Ramones)
Have I done something wrong with my simulation? If that's the case, then this is my mdp parameter:
cpp = /lib/cpp
include = -I../top
integrator = md
dt = 0.002
nsteps = 10000
nstxout = 100
nstvout = 100
nstlog = 1000
nstenergy = 100
nstxtcout = 100
xtc_grps
= System
energygrps = System
nstlist = 10
ns_type = grid
rlist = 1.0
; PME chosen as the best option to calculate viscosity ;
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.4
pbc = xyz
tcoupl = berendsen
tc-grps = System
tau_t = 0.1
;
temperature supposed to set to 20*C @ 293.15 K as reference work ;
ref_t = 293.15
Pcoupl = no
gen_vel = yes
gen_temp = 298.15
gen_seed = 173529
constraints = none
; NEMD ;
acc_grps = system
accelerate = 0.1 0.0 0.0
cos_acceleration = 0.02
Any suggestion are most welcomed and thank you in advance!
MUHAMMAD ALIF MOHAMMAD LATIF
Laboratory of
Theoretical and Computational Chemistry
Department of Chemistry
Faculty of Science
Universiti Putra Malaysia
43400 UPM Serdang, Selangor
MALAYSIA
