[gmx-users] density

Sunil Thapa mephysik at yahoo.com
Wed Feb 24 13:23:46 CET 2010

Respectable Experts
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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