[gmx-users] Re: NEMD

[Junqiao Lee]

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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