Respectable Experts
Grettings
I am studying diffusion of an oxygen molecule in 255 molecule of SPC water. I
need to determine diffusion coefficient at temperature 298 K and 1 atm
pressure. In order to do that
using editconf I scaled the density of the system including oxygen to 1g/l. I
checked the density after energy minimization (steepest descent) which gave the
reading of 0.76 g/l. After that I equilibrated the system to pressure of 1 bar
and temperature of 298 K using NPT simulation (berendsen). The density reading
was 0.98. When I checked the density table at 298 K, it was about 0.9927 g/l.
I am afraid if my density is not consistent with experimental density of the
system. Is this some bug of gromacs 3.2.1 or my understanding of thermodynamics
is very poor for pressure and liquid density. Please help me on this.
Should I use the same NPT simulation to derive the experimental diffusion
coefficient ?
Looking forward to hearing from you
Neal, Nepal
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