Transverse Current Autocorrelation Function, FV and FFV

User discussions
1

GROMACS version: 2023.1
GROMACS modification: No

Hello.

I run 100 ns md and make last 40 ns trajectory file, for analysis, in order to reduce computational power.

  1. How can I use that last-40ns.xtc file to obtain transverse current autocorrelation function and evaluate shear viscosity of the system?
    Shortage of memory prevents me from using “gmx tcaf md.cpt -s md.tpr”
    Energy module produce unacceptable result of viscosity.

  2. I performed two types of simulations: pure compound and compound with CO2. I use the same box size but during analysis the box volume, free volume and fractional free volume of the second system (compound with CO2) were higher. Is this result valid and how can I explain it?

Thank You.

2

PS:

  1. Now tcaf command with md.trr instead of md.cpt works well.
    But still need idea on how to extract and analyze the tcaf output data example below
Selected 0: 'System'
trr version: GMX_trn_file (single precision)
Last frame      10000 time 100000.000   
Density = 990.032 (kg/m^3)
Average correlation time 350099.219 Std. Dev. 827455.375 Error 104249.578 (ps)
k  1.222  tau  0.092  eta  0.29123 10^-3 kg/(m s)
k  1.222  tau  0.088  eta  0.44193 10^-3 kg/(m s)
k  1.222  tau  2.051  eta  0.14956 10^-3 kg/(m s)
k  1.728  tau  0.065  eta  0.97741 10^-3 kg/(m s)
k  1.728  tau  0.087  eta  0.23458 10^-3 kg/(m s)
k  1.728  tau  0.093  eta  0.12313 10^-3 kg/(m s)
k  1.728  tau  1.965  eta  0.07743 10^-3 kg/(m s)
k  1.728  tau  0.060  eta  0.98203 10^-3 kg/(m s)
k  1.728  tau  0.090  eta  0.17020 10^-3 kg/(m s)
k  2.116  tau  0.049  eta  0.78798 10^-3 kg/(m s)
k  2.116  tau  0.118  eta  0.44864 10^-3 kg/(m s)
k  2.116  tau  0.033  eta  1.42568 10^-3 kg/(m s)
k  2.116  tau  0.089  eta  0.13262 10^-3 kg/(m s)
k  2.444  tau  0.091  eta  0.07491 10^-3 kg/(m s)
k  2.444  tau  0.045  eta  0.93633 10^-3 kg/(m s)
k  2.444  tau  0.088  eta  0.11086 10^-3 kg/(m s)
  1. From the density plot, I discover that the second simulation reach equilibrium around first 25 ns. Therefore, I performed the analysis from that region to the end. The FV and FFV become lower than that of the first case.