[gmx-users] Best Force Field for a Membrane Protein

Anirban Ghosh reach.anirban.ghosh at gmail.com
Thu Apr 19 08:32:36 CEST 2012


When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or
DPPC etc.) which according to your experience is the most suited
force-field in GROMACS that best retains the 7TM / secondary structures of
the protein over long simulations? I have tried running with ff53a6 (as
suggested in Justin's tutorial), but find that the helices in the bilayer
tend to lose their helicity over time and turns into coils. ff43a2 seems to
do the job somewhat better by retaining the helicity. Will ff43a1 work even
better as the principle aim is to observe changes in the protein without
losing its secondary structures? Your experience please.
Thanks a lot in advance.


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