[gmx-users] Frozen atoms and energy group exclusion

[toma0052]

Hello,
     Thanks for the fast response.  I went through my dppc.itp file and chose
atoms such that the group of frozen atoms has a net charge of 0 as does the
rest of the molecule.  When running this through grompp, the error before
about the atoms being in different charge groups is gone.  However, the
warning (WARNING 1 [file "dppc.top", line 19]: Can not exclude the lattice
Coulomb energy between energy groups) is still present.  What exactly does
this warning mean?  Will this have a large affect on my simulation output?

Mike Tomasini




On 5 Mar 2007, Mark Abraham wrote:
> >      When I run this through grompp, I get the following error:
> > WARNING 1 [file "dppc.top", line 19]:
> >   Can not exclude the lattice Coulomb energy between energy groups
> > Checking consistency between energy and charge groups...
> > -------------------------------------------------------
> > Program grompp, VERSION 3.3
> > Source code file: grompp.c, line: 307
> >
> > Fatal error:
> > atoms 3212 and 3213 in charge group 2179 are in different energy groups
> > -------------------------------------------------------
> >
> > Am I doing this incorrectly?  Should I be excluding the interactions wi=
> th
> > the
> > frozen groups in another way?
> 
> Have a look at the description of charge groups in 4.6.2 and 4.6.3 and th=
> e
> implementation of this in 5.5.1. grompp is evidently complaining that you=
> r
> charge group boundaries are not the same as the energy group boundaries,
> and since non-bonded energies are calculated looping over charge groups,
> this is a fine thing for it to be unhappy about! So have a look at the
> charge groups in your DPPC molecule and see if you can come up with a
> compromise that keeps charge group neutrality.
> 
> Mark
> 
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