[gmx-users] RE: .rtp libraries

Tsjerk Wassenaar tsjerkw at gmail.com
Thu May 13 12:50:23 CEST 2010

Hi Stephen,

> I am particularly interested in lipid .rtp libraries hopefully for something that has all-atom force fields, as I personally believe simulations should be as real as possible, and also believe non-polar hydrogens still illicite some force in the overall scheme of the molecular simulation.

Yes, of course they do. And don't forget charge transfer effects,
polarization and quantum effects. But you can't have it all. Every
model has its domain of application and its pros and cons.

> As most lipid systems in cells are insanly complec, many lipid types in many proportions and chain lengths, etc... I woundered if somone(s) has already constructed a library with the 200 or so outer membrane lipids.  I did read years back about mitochondrial simulations, which did include dozens of lipids, even cardiolipin, etc...but never found libraries.

References would be good. I know there's a good deal of effort on
parameterization of lipids, especially in the group of Tieleman, as
well as in ours. But an encompassing library of lipid models seems to
be a bit too much to ask for at the moment. Parameterization is a
tricky process, especially if the experimental data on pure lipids and
controlled mixtures is scarce. Any such library should be used with
caution, i.e. with background reading of the methods and assumptions
used for the parameterization.

> Happy Ascention

Errm, I wasn't intending on going yet... :p



Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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