[gmx-users] lipid.itp and grompp

[Peter Tieleman]

Hi all,

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.

Peter

--
Dr. D.P. Tieleman, Assistant Professor, AHFMR Scholar
Department of Biological Sciences, University of Calgary
2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
web: www.ucalgary.ca/~tieleman  fax: (403)289-9311 tel: (403)220-2966