[gmx-users] Water models and diffusion coefficient
joinforfun8909 at gmail.com
Sat Feb 9 14:21:48 CET 2013
I am simulating a model of heavy water, with charges modified from SPCE
model. This was proposed by Grigera , with H replaced by D and
charges on O and H increased from values proposed in SPCE model.
I have verified by using gmxdump that gromacs sees the mass of H as 2.014
amu and the charges as specified in the topology file. The density comes
out as expected for heavy water. The system equilibrates well (well-defined
fluctutations, no trends in energy, density, pressure, temperature)
However, the diffusion coefficient is always lower than that expected for
the model. By using the same parameter files I ran a simulation for normal
water (SPCE) model and the diffusion coefficient matches with that reported
from other simulations.
Is there something else that I should check? or is there something about
g_msd that I am missing?
Any pointers would be really helpful.
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