There have been several bug fixes related to viscosity calculations since the
release of version 4.5.3, of which at least one (on 1/10/2011) specifically
mentions zero viscosity in the .edr and .log files.
I would suggest pulling the latest release-4-5-patches from the git repository
and try again.
-Justin
Xiang Gu wrote:
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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