[gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins
samuli.ollila at aalto.fi
Wed May 7 14:59:30 CEST 2014
In my understanding the CH2-LP2 attraction is stronger than LP2-LP2 attraction in the Berger/Höltje combination you described. If you then have CH2 groups in cholesterol and LP2 groups in lipids, it might lead to too condensed bilayer. I think that the related issue is discussed here:
we have changed the CH2 groups in cholesterol to LP2 groups and compared the results quite extensively to the NMR measurements.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of David Ackerman [da294 at cornell.edu]
Sent: Monday, May 05, 2014 7:39 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins
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 (
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
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