[gmx-users] Water models and diffusion coefficient

Joinforfun Doe 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 [2001], 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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