[gmx-users] the issue of calculation of viscosity with NEMD

[David van der Spoel]

On 2015-02-12 02:10, 陈思言 wrote:
>
>     csy12 at mails.jlu.edu.cn <mailto:csy12 at mails.jlu.edu.cn>
>
>         Dear gromacs users:
>
>         ​
>
>         I have an issue when I calculate the viscosity with NEMD.
>
>         Why the value of 1/viscosity obtained by g_energy in GROMACS
>         remains zero when calculating viscosity with NEMD?
>
you mean 0.0?
or almost 0?
It worked last time I tried it (2003).

>         The mdp file is below:
>
>         title = production-run
>         cpp = /lib/cpp
>         define =
>         constraints =
>         integrator = md
>         dt = 0.001 ; ps !
>         nsteps = 80000
>         nstcomm = 1
>         nstxout = 100
>         nstvout = 100
>         nstxtcout = 5000
>         nstfout = 0
>         nstlog = 10000
>         nstenergy = 100
>         nstlist = 1
>         ns_type = grid
>         ; Periodic boundary conditions: xyz or no =
>         pbc = xyz
>         rlist = 1.3
>         rcoulomb = 1.3
>         rvdw = 1.3
>
>         ; OPTIONS FOR ELECTROSTATICS AND VDW =
>         ; Method for doing electrostatics =
>         coulombtype = PME
>         ; Method for doing Van der Waals =
>         ;;;;;;;;;;;;;vdw-type = Switch
>         ; cut-off lengths =
>         ;;;;;;;;;;;;;;;;rvdw-switch = 1.3
>         ; Apply long range dispersion corrections for Energy and Pressure =
>         DispCorr = EnerPres
>         ; Spacing for the PME/PPPM FFT grid =
>         fourierspacing = 0.08
>         ; FFT grid size, when a value is 0 fourierspacing will be used =
>         fourier_nx = 0
>         fourier_ny = 0
>         fourier_nz = 0
>         ; EWALD/PME/PPPM parameters =
>         pme_order = 6
>         ewald_rtol = 1e-05
>         ewald_geometry = 3d
>         epsilon_surface = 0
>         optimize_fft = yes
>         ; Nose-Hoover temperature coupling is on
>         Tcoupl = berendsen
>         tc-grps = PF6 c10
>         tau_t = 0.05 0.05
>         ref_t = 300.00 300.00
>         ; Energy monitoring
>         energygrps = PF6 c10
>         ; Pressure coupling is on
>         Pcoupl = no
>         tau_p = 1.0
>         ;Non-equlibrium MD
>         cos_acceleration = 0.06
>         ; Generate velocites is on at 300 K.
>
>         gen_vel = no
>
>         gen_temp = 300.00
>         gen_seed = 273529
>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se