[gmx-users] A question regarding electrostatic and coulomb energies.

[Mark Abraham]

On Mon, Feb 9, 2015 at 12:40 PM, IÑIGO SAENZ <
inigo.saenz01 at estudiant.upf.edu> wrote:

> Dear Mark,
>
> I've been researching about energy groups and I think that it isn't the
> solution for my problems.
> The background of my question is the following:
> I'm currently working with the people that develops ACEMD and because of
> that I've got access to some information that ACEMD uses for its
> calculations.
> For each system that I simulate, I've got the list of all the pairs of
> atoms that must be excluded in the nonbonded calculations (e.g. atoms that
> are bound, 1-3 bound atoms and so on)
> On the other hand, I also have a list of all the pairs that must be
> included in the nonbonded calculations (1-n bound atoms, for n>=4 and so
> on)
>

grompp handles these details in response to the nrexcl setting in the .top
- there's a few lines of docs in chapter 5 somewhere.


> The point is that I need to use that information (and more info that ACEMD
> provides me) to generate a .gro and .top file in order to be able to run
> the systems both in ACEMD and in Gromacs.
>
> When I perform a SPE of a system in both ACEMD and Gromacs, the bond, angle
> and dihedral energies are approximately equals in both, but Coulomb and VDW
> energies are very very different and this is driving me crazy.
>

I think this has come up on the list before, perhaps even with ACEMD.
Recent versions of GROMACS, particularly with the Verlet cutoff scheme,
shift the potential across its whole range by the value it takes at the
cutoff, so that it is the integral of the force. Not all packages do this,
but you have to do it consistently if you want the comparison.

Mark

Hoping that you can help me, if any of you need more information about the
> .gro, the .top or the information that ACEMD provides me, don't hesitate in
> contact me.
>
> Thank you very much in advance.
>
> Iñigo S.
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