[gmx-users] distance dependent energy

[Cuong Nguyen]

Thank you Mark and Erik,
Van

On Wednesday, 23 September 2015, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Tue, Sep 22, 2015 at 5:47 PM Cuong Nguyen <nvcuong68 at gmail.com
> <javascript:;>> 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.
>
> Mark
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-- 


Cuong Van Nguyen (PhD Student)
Department of Chemical Engineering
Curtin University, Western Australia
Tel. (+61) 45 221 3981