[gmx-users] Viscosity calculation problems (periodic perturbation method)

[Xiang Gu]

Hi, all,

I was trying to reproduce the viscosity results of SPC water reported in 
Berk Hess' paper (JCP, vol.116 No.1, 209-217, 2002) by using the 
periodic perturbation method. After reading some old tips on the 
maillist exchanged by Song, David, etc., I tried to set up the NVT 
simulation just according to Hess has done, and sent it to calculation.

Probably because not everything is properly understood, I processed the 
edr file with g_energy_d but found both the columns 2CosZ*Vel-X & 
1/Viscosity always zero. I played with several options of Tcoupl and 
tau_t, still the same happened. Could anybody experienced in this tutor 
me what has been improperly specified in the mdp file (see below; system 
is 3456 SPC water molecules contained in a 3.75*3.75*7.5 nm^3 box--just 
as in Hess' paper Table II, already well equilibrated at 300 K in 
advance; perhaps it is unnecessary to run this double precisely, but I 
was using double precision version (4.5.3.d) just because I forgot to 
switch to the single precision one, however this shouldn't cause the 
problem I had ...)?

Thanks and wish to see your suggestions soon!

Xiang Gu

;    Generic mdp file for SPC water equilibration
;    Gromacs 4.3.x
;
;    T = 300 K
;
;    NVT equilibration run, 1.2 ns
;

define               =              ; define here posres etc., e.g. -DPOSRES

integrator              = md
tinit                   = 0
dt                      = 0.001
nsteps                  = 1200000

; Bond constraints
continuation            =  no          ; switch to 'yes' if need to read 
in velocities etc.
constraints             =  none        ; constrain all bond lengths
constraint_algorithm    =  lincs       ; default
lincs_order             =  4           ; default

; X/V/F/E outputs ---- change these according to your system ----
nstxout                 = 1000
nstvout                 = 1000
nstfout                 = 0
nstlog                  = 1000
nstenergy               = 1000
; Output frequency and precision for xtc file
nstxtcout               = 1000
xtc-precision           = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps                =
; Selection of energy groups
energygrps              = System

; Neighbor list
ns_type              =  grid        ; neighlist type
nstlist              =  5           ; Freq. to update neighbour list
rlist                =  0.9         ; nm (cutoff for short-range NL)
pbc                  =  xyz         ; xyz(default), no, full(infinite 
systems)
periodic_molecules   =  no

; Non-equilibrium MD
;acc_grps             = SYSTEM
cos_acceleration     =  0.025       ; PPM option for viscosity 
calculation (nm/ps²)

coulombtype          = PME
rcoulomb             = 0.9
optimize_fft         = yes             ; affects only PME calculations
                                       ; if you use PME, set also 
rcoulomb = rlist

; van der Waals interactions
vdwtype              =  Cut-off        ; Van der Waals interactions
rvdw                 =  0.9            ; nm (LJ cut-off)
DispCorr             =  EnerPres       ; long-range dispersion 
correction to energy and pressure

Tcoupl                  = berendsen
tc-grps                 = System
tau_t                   = 2.5
ref_t                   = 300.0

;Pressure coupling
Pcoupl              =  no              ; berendsen, tau_p = 1.0 for 
faster equilibration
;Pcoupltype          =  isotropic       ; semi-isotropic: xy and z 
separately (CNT)
;tau_p               =  1.0             ; ps
;compressibility     =  4.5e-5          ; 1/bar (water @ 1 atm, 300 K)
;ref_p               =  1.0             ; bar0  4000 1.034798 0.001949

gen_vel                 = no
;gen_temp                = 300.0
;gen_seed                = 173529

-- 
_____________________________________________________
Xiang Gu, PhD, Postdoctoral Research Fellow
Department of Applied Physics
Aalto University School of Science and Technology, Finland
Tel: +358-9-470 23137
Email: xiang.gu at aalto.fi
http://tfy.tkk.fi/soft/