[gmx-users] Re: Water models and diffusion coefficient

Dr. Vitaly Chaban vvchaban at gmail.com
Sat Feb 9 18:16:10 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.

I did not the frequency of saving coordinates for g_msd in your case,
but if you save them too rarely, it will give smaller diffusion
coefficient then it really is in MD.

Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark

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