To whom this may concern,
I have been trying to find documentation for the gmx dipoles and gmx dielectric
functionalities in GROMACs and have found that what is out there is remarkably
sparse.
I would really appreciate some clarification on what each of these
functionalities actually do. As far as I can tell, the gmx dipoles outputs two
files that are of interest if you want to calculate the static dielectric
constant:
Epsilon(0) = 1 + 4 Pi/3 * (<M^2> - <M>^2)/(V k_B T)
where M is the systems total dipole moment, V is the system volume, k_B is the
Boltzmann constant, and T is the system temperature.
The first file is aver.xvg which outputs the averages for the total dipole
moment M. Is this a cumulative average of the systems (based on your index
selection) total dipole moment and related values?
The second file is epsilon.xvg.
1. Is the epsilon value in this file a cumulative average as well?
2. Is it the static dielectric constant or something else?
3. If it is the static dielectric constant, what Volume is used? Is it the
systems average volume up to that point (which becomes important in NPT
simulations) or is it the systems average volume over the entire simulation?
Although rigorously the dielectric should be calculated on simulations in the
NVT simulation, it is of interest to know how the volume is handled when in an
NPT simulation.
The gmx dielectric functionality is also a bit confusing since it is not
entirely clear what is being calculated there. Is gmx dielectric's aim to
calculate the frequency dependence of the dielectric constant? And if so, how
is that executed?
Best Regards,
Lara Patel
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