[gmx-users] Some important information about setting up gromacs topologies

[Marc Baaden]

Hi,

as you have obviously noticed by me polluting the mailing list with
questions about gromacs topologies, I have been working on this quite
intensely over the last days.

With the help of some of the Gromacs developers, it has shown that one
has to take special care with nonbonded parameters when setting up
a topology.


The quintessence is, that if you want to make sure everything goes
smoothly, you should only have one [ atomtypes ] and one [ nonbond_parms ]
section, and in precisely this order.

This means, if you need new atomtypes, you have to define them in the
actual ffXXnb.itp file, as well as any LJ pairwise interactions that
are different from what the combination rule would yield.


You should check all your included itp files precisely and make sure that
they do not contain any further [ atomtypes ] or [ nonbond_parms ]
section ! Eg if you want to use methanol or flexwat-ferguson in combination
with anything else, you should modify these itp files and add the atom-
types to the forcefield you want to use.


I think an improved (more permissive) version of grompp is under way
and more detailed comments were added to the latest manual version,
but check with the developers if you want more details.

  Marc Baaden

-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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