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

Reid Van Lehn rvanlehn at mit.edu
Sat Feb 9 16:28:26 CET 2013

What time period do you use to fit the mean-squared displacement to
determine the diffusion coefficient? g_msd determines the diffusion
coefficient by performing a linear fit over the time interval specified by
the -beginfit and -endfit flags, which default to 10% and 90% of the
simulation time (if I remember correctly) if you do not specify values. If
your mean-squared displacement is not linear over this interval, then you
could have a very poor estimate of the diffusion coefficient. You might to
look at the plots of the MSD generated to see if it is linear over the
interval you fit; if it plateaus over this period then likely the diffusion
coefficient is an underestimate, and since the value you measure is
relatively close to the literature value then that could explain the lower

- Reid

On Sat, Feb 9, 2013 at 9:12 AM, learnmd <joinforfun8909 at gmail.com> wrote:

> Thanks for your reply David. However, what I am concerned is that with the
> parameters, q[O] = -0.870, and q[H] = 0.435, the original author reported
> diffusion coefficient very close to 2.0 e-5 cm^2/s. My values for even much
> longer simulations (200 ns after 1ns each of NVT and NPT equilibration)
> reports diffusion coefficients which are always much lesser ( in the range
> 1.4 - 1.5 e-5 cm^2/s).
> I was wondering if there is something that I should understand better about
> g_msd not getting the right mass of H atoms?
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> Reid Van Lehn
> NSF/MIT Presidential Fellow
> Alfredo Alexander-Katz Research Group
> Ph.D Candidate - Materials Science
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