Dear all, I am working on clay in water box. I have fixed the COM of clay, by grouping the clay atoms and applied the following command.
I have this clay surrounded by water molecules in simulation box of 60 angstrom cube.
I am trying to find thermodynamic parameters such as diffusion coef, viscosity, rdf , etc, of water.
Is it necessary to fix COM of box also? Does it give wrong data?
Kindly suggest me.
group clay type 1 2 5 6
group water type 3 4
velocity all create 298 123456 rot yes mom yes dist gaussian
fix 1 all npt temp 298 298 100 iso 1 1 1000
fix COM clay recenter INIT INIT INIT units box
fix 2 all rattle 0.0001 50 0 t 3
compute cc1 water chunk/atom molecule
compute omega water omega/chunk cc1
fix 3 water ave/time 5000 1 5000 c_omega[*] file omega-3.out mode vector
compute msd water msd/chunk cc1
fix 4 water ave/time 5000 1 5000 c_msd[*] file msd-3.out mode vector
compute rdf all rdf 5000 4 2 4 4 4 5 4 6 5 3
fix rdf all ave/time 5000 1 5000 c_rdf[*] file rdf-3.out mode vector
timestep 0.1
run 10000
You built your Model in Matlab Simulink , before import your file and data you first prepare your datasets according to the requirement and then find out in matlab simulink
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