[gmx-users] GAFFlipids for Gromacs?

Ollila Samuli samuli.ollila at aalto.fi
Thu Oct 3 13:38:48 CEST 2013

Dear Gromacs users,

I have recently written a manuscript titled:  "Response of the hydrophilic part
of lipid membranes to changing conditions — a critical comparison of
simulations to experiments" (http://arxiv.org/abs/1309.2131). To rapidly
improve the manuscript further, we started a public blog


Everyone who contributes to the blog will become author of the final publication
(for more details see the post "On credits" in the blog).

The final goal of this open collaboration is to find an atomistic (prefentially united
atom) force field that correctly describes the headgroup and glycerol parts of a
phosphatidylcholine lipid bilayer, in particular as it responds to changing
conditions: hydration, salt, cholesterol, ... The validity of the model is tested
against order parameters measured by NMR.

As described in the blog, currently there seems to be three force fields that
reproduce the NMR glycerol and headgroup order parameters for pure bilayers under
full hydration. One of these is GAFFlipids (Dickson et al. Soft Matter, 2012, 8, 9617).
Our next step is to test the behaviour under changing conditions.

My question now is: Have you ran simulations with GAFFlipids in Gromacs
and if so, would you be willing to share your topology and initial structure
with us in the blog?

This contribution would be very helpful for the collaboration, so if you think
you could help, we keenly look forward to hearing  from you.

Samuli Ollila

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