[gmx-users] Re: NEMD

[Junqiao Lee]

I seem to be able to extract the viscosity by specifying "*-vis
visco.xvg" *when
running g_energy -- averaging of the 3rd Column to give the "bulk viscosity"
(cp).
Selecting *2CosZ*Vel-X *and *1/Viscosity *from the list when running
g_energy w/o the -vis output parameter doesn't seem to be working(?). I'm
now using the latest Gromacs 4.5.3.

Also, the "blowing up" of my system appear to be quite random, where there
can be two runs with exactly the same parameters, where one blows-up (i.e.
density --> 0) while the other one don't. My cos_acceleration = 0.03 model
exploded, while cos_acceleration = 0.2 which I earlier though would, didn't.

On Sun, Nov 14, 2010 at 3:28 AM, Junqiao Lee <aeondrift at gmail.com> wrote:

> Hi,
>
> *Here's to tidy up my earlier query which has gotten a bit messy -- to
> include the earlier previous relevant informations that were asked, and to
> provide additional relevant informations.*
>
> I've tried running NEMD test-runs in NPT vis initially setting the "cos_acceleration
> = 0.3" (nm ps^-2) parameter to determine the solvent viscosity.
> However my system kept spectacularly exploding. My system is stable under
> normal MD (up to 30% over its empirical boiling point at 490K).
>
> My system is stable when cos_acceleration is below ~0.05, etc. *However I
> still keep getting ZERO for **both 2CosZ*Vel-X and 1/Viscosity* out of all
> the test runs (including those that exploded) as showing below in the
> g_energy output and also in the .xvg file.
>
> Statistics over 3515501 steps [ 2000.0000 through 9031.0000 ps ], 20 data
> sets
>
> All statistics are over 351551 points
>
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
>
>
> -------------------------------------------------------------------------------
>
> Angle                       2105.24        1.9    74.6742    11.9145
>  (kJ/mol)
>
> Fourier Dih.               -129.198         11    58.6995   -58.4497
>  (kJ/mol)
>
> ...
>
> Total Energy               -64836.9        7.5     192.87   -45.1406
>  (kJ/mol)
>
> Temperature                 297.941      0.012    6.87995  -0.042248  (K)
>
> Pressure                    1.02384      0.025    381.044 -0.0603063  (bar)
>
> Volume                      42.8729     0.0059   0.468899 -0.00248636
>  (nm^3)
>
> Density                     940.264       0.13    10.2704  0.0530898
>  (kg/m^3)
>
> Enthalpy                   -64836.6        7.5     192.87   -45.1406
>  (kJ/mol)
>
> *2CosZ*Vel-X                       0          0          0          0
>  (nm/ps)*
>
> *1/Viscosity                       0          0          0          0  (m
> s/kg)*
>
>
> ---------------------------------
>
> integrator               = md
> dt                       = 0.002
> nsteps                   = 100000
> comm-mode                = Linear
> nstcomm                  = 10
> nstxout                  = 10000
> nstvout                  = 10000
> nstfout                  = 0
> nstlog                   = 500
> nstcalcenergy     = 250
> nstenergy                = 500
> nstxtcout                = 500
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> coulombtype              = pme
> rlist                    = 1.0
> rcoulomb                 = 1.0
> vdw-type                 = Cut-off
> rvdw                     = 1.0
> pcoupl                   = Parrinello-Rahman
> pcoupltype               = isotropic
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 0.5
> Tcoupl                   = v-rescale
> tc_grps                  = System
> tau_t                    = 0.1
> ref_t                    = 298
> gen_vel                  = no
> gen_seed                 = 94839
> constraints              = All-bonds
> constraint-algorithm     = lincs
>
> *cos_acceleration = 0.05*
>
>
> Are there anything that I need to set to get non-zero output values?
>
> Cheers,
> Junqiao LEE (Wade)
>
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