[gmx-users] Rigid water model

Mark Abraham mark.j.abraham at gmail.com
Sun Mar 16 14:33:07 CET 2014

On Mar 14, 2014 11:06 PM, "Michelle Aranha" <maranha at utk.edu> wrote:
> Hi!
> I tried to reproduce results for rigid water with 895 molecules~1000 kg/m3
> density, 10 ns NPT simulation (298 K & 1 bar)with Parinello Rahman
> and Berendsen thermostat.

Using a thermostat that produces the wrong velocity distribution is asking
for trouble. No idea if that's your main problem, though.

> Here is my result for SPC water
> Kappa (J/m3)    5.689E-10
> Cp      22.8054
> Cp- Cv  5.94102
> The density, diffusion coefficient, the average configuration energy agree
> with previous results. However the heat capacity value is quite low as
> compared to 75 J/mol K of real water or even that has been previously
> with water models. I compared my values with a 2 ns and 10 ns simulations,
> but the heat capacity value shows no real improvement. I do not know much
> about quantum corrections hence I have not tried it. Will applying quantum
> corrections give the correct heat capacity?
> The isothermal compressibility  reported by GROMACS is in J/m3 and the
> adiabatic bulk modulus is reported in m^3/J, could that be a mistake and
> should it be rather in  (J/m^3)^-1 and J/m3 respectively.
> And, why does the isothermal compressibility change during the course of
> simulation if it has been fixed in the mdp file.

A parameter for an algorithm and an observed property are two different


> Best wishes,
> Michelle
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