[gmx-users] Gromos force fields and simulation of the alpha-helices membrane proteins

James Starlight jmsstarlight at gmail.com
Fri Sep 21 20:33:31 CEST 2012

Dear Gromacs Users!

In some recent publications about protein dynamics investigation I've
found reference about new gromos force field (56A7) where some fix in
case of dihedral terms have been included.

During my simulation performed with the 56A6 ff I've noticed that in
some cases short alpha helices fragments were unfolded during 50-100ns
of simulation. In particular that was in cases of simulation of
membrane receptors. In some of that proteins I've observed unfolding
of the part of the alpha helices which were placed in the water layer
( the rest of the alpha helices embedded in the membrane layer was
very stable during all simulation time ). So I wounder to know if that
events were the artifacts of the 56A6 force field or there are some
biological-significance of such dynamics seen in the water layer.
Is it possible to obtain new 56A7 ff and integrate it into Gromacs (
I'm using version 4.54). ?

Will the systems (topologies) made for 56A6 ff compatible with the
56A7 ff ( In particular I'm using Berger's lipids) or should I create
my protein-in-membrane system again ?

Thanks for help,


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