[gmx-users] distance dependent energy

Mark Abraham mark.j.abraham at gmail.com
Tue Sep 22 20:53:15 CEST 2015


On Tue, Sep 22, 2015 at 5:47 PM Cuong Nguyen <nvcuong68 at gmail.com> wrote:

> Dear Gromacs users,
> I would like to work out the energy (total and kinetic) as a function of
> the distance from the center of mass of a droplet. However, using g_energy
> just gave me the values as a function of time. Could anyone tell me the way
> to get the distance dependent values?

First, you'd have to record them. mdrun doesn't work by first evaluating a
giant matrix of per-anything energies, and then adding them up. You can use
energy groups to break down the short-ranged non-bonded component of the
potential energy into intra- and inter-group terms, but you can only have
256 of them, and only with the group scheme, and only if you're not
concerned about diffusion (or are prepared to use dynamic selections and
mdrun -rerun creatively). And the work you have to put in to get that out
is not really worth thinking about unless you know exactly what you're
going to learn from the result.


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