[gmx-users] Viscosity calculation using cos_acceleration

[Berk Hess]

Hi,

I "fixed" an issue with the 1/visc output in 4.5.4, but incorretly.
I filed a bug report and a fix, you can easily correct your numbers:
http://redmine.gromacs.org/issues/1244
https://gerrit.gromacs.org/#/c/2370/

Thanks for reporting this.

Cheers,

Berk

> Date: Thu, 11 Apr 2013 16:55:37 +0900
> From: jamesresearching at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Viscosity calculation using cos_acceleration
> 
> Dear Gromacs users,
> 
> This question seems to come up periodically in the mailing list, but none
> of the previous answers seem helpful in my case.
> 
> I'm trying to reproduce the viscosity calculation of SPC water by Berk Hess
> (JCP 116, 2002) using cos_acceleration in Gromacs. The answer I get is 2
> orders of magnitude out.
> 
> My topology file and parameter file is appended at the bottom of this email.
> 
> I run g_energy and get
> 
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> 1/Viscosity                 23.4689       0.13    2.39126  -0.255371  (m
> s/kg)
> 
> which gives a viscosity of 0.04 kg/(m s), or 40 mPa.s
> 
> The value quoted in the paper is about 0.4 mPa.s which is around the
> correct value for water, give or take a bit.
> 
> So my question is, where is my missing factor of 100?
> 
> Any advice is much appreciated.
> 
> Thank you.
> 
> James
> 
> --------------------------
> Topology file:
> #include "ffgmx.itp"
> #include "spc.itp"
> 
> [ system ]
> Pure Water
> 
> [ molecules ]
> SOL     3456
> 
> --------------------------
> Parameter file for system (3456 SPC water molecules, 3.75x3.75x7.5 nm3 box):
> 
> ;    Generic mdp file for SPC water equilibration
> ;    Gromacs 4.3.x
> ;
> ;    T = 300 K
> ;
> ;    NVT 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
> 
> 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
> 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
> gen_vel                 = no
> -- 
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