[gmx-users] lipid.itp and grompp

Erik Lindahl lindahl at stanford.edu
Sat Apr 6 20:46:23 CEST 2002


> Marc Baaden's warning about the somewhat unexpected behavior of grompp when
> having multiple atomtypes and non-bonded entries applies to using lipid.itp
> too. In the way I set it up, the LJ interaction matrix in the GROMOS based
> force fields (ffgmx in this case) is overwritten with standard combination
> rules. I don't yet know what the effect is of this. It means the force field
> isn't used the way it was designed. On the other hand, nearly all published
> simulations on membrane proteins with gromacs will have used the combination
> rules for the protein part instead of the GROMOS values, often without
> disastrous consequences.
> To use the protein-protein GROMOS LJ parameters, the contents of lipid.itp
> should be copied into the ffgmx* files as Marc described. It should be
> possible to test the differences on simulations of high-resolution membrane
> protein structures.

This is definitely a bug that should definitely fix; the immediate 
solution is to give a warning if there's more than one atom or 
nonbonded-parameter section, and then we'll have think of the proper way 
to treat topologies with more than one section...

Almost everything in GROMOS96 is based on combination rules though; the 
only exception is some of the C12 paratermer where another atom 
interacts with water oxygen atoms, and the difference isn't large.



More information about the gromacs.org_gmx-users mailing list