[gmx-users] a few detailed questions about the topology file format

Mark Abraham mark.j.abraham at gmail.com
Thu Jul 30 13:48:12 CEST 2015


On Wed, Jul 29, 2015 at 9:39 PM Eric Smoll <ericsmoll at gmail.com> wrote:

> Hello Gromacs users,
> As far as I understand, values listed in the top file override any
> information pulled from share/gromacs/top. However, ff an atom type (e.g.,
> "opls_100") serves as a references to information contained in the
> share/gromacs/top directory, is it necessary to include a value for the
> charge in a itp/top file?

I don't know if per-atomtype charges in the database can ever be used -
such a field would only make sense for quite simple models. Try leaving the
charge blank in your .top and observe what happens, e.g. with gmx check to
compare two .tpr files.

It seems that the corresponding entry in
> ffnonbonded should supply this information. Going further, what is the
> minimal amount of information necessary in the atoms directive?

I do not think a clear definition exists. This is part of the price of a
tool that can be used for many things. (And probably there is also design &
implementation legacy for things that are no longer used/useful.)

> The gromacs manual includes an example topology for urea. The bonds
> directive only lists pairs of atom indices. When the function type is not
> listed, does it default to "1"?

I doubt it, but often you'll get a faster and more accurate answer from
trying things out :-) Software that grew over decades written by multiple
authors with no spec is... messy.


> Eric
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