[gmx-users] Re: Adding a new water model to gromacs

learnmd joinforfun8909 at gmail.com
Sun Jan 20 18:06:37 CET 2013

I added the heavy water model to amber94. Essentially I replaced all masses
of H to mass of Deuterium everywhere in the ffbonded.itp and
ffnonbonded.itp as well as spc.itp. The density of the system comes out
correctly as 1124.28 kg/m^3, which corresponds to density of D2O at 300 K.

So, I think that the system is counting the mass of H correctly as that of
D. The simulation has 902 molecules of D2O in a 27 nm^3 box. I am running
NPT simulations at 300 K. However, the Diffusion constant from g_msd comes
out as 1.4818 (+/- 0.1201) (1e-5 cm^2/s), which corresponds to H2O.
Simulations report MSD of D2O as 2.0 e-5 cm^2/s.

Any suggestions on what I may have overlooked or am doing wrong. I am using
the isothermal compressibility of D2O in my mdp file for running MD

Thanks a lot.

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