[gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins

David Ackerman da294 at cornell.edu
Mon May 5 06:45:58 CEST 2014


I have been performing simulations of multi-component bilayers using
parameters described in the following paper:
http://www.ncbi.nlm.nih.gov/pubmed/23470157. They use the ffgmx forcefield
with Berger lipid parameters included. They also use cholesterol from
Holtje et. al (
http://www.sciencedirect.com/science/article/pii/S000527360100270X), which
was parameterized for the ffgmx force field.

I noticed that unlike the KALP-15 GROMACS tutorial which suggests deleting
the default lipid-gromos Berger interactions, the authors kept those
interactions in the force field. In light of newer force fields, are these
older force fields wither Berger parameters still acceptable? The
cholesterol model seems commonly used, so I am unsure how to use
cholesterol with a newer force field.

Furthermore, if I were to include proteins in the simulation, would I still
be able to use the same ffgmx force field with Berger parameters (including
lipid-gromos interactions)?

Thank you,

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