[gmx-users] NM and energy minimization

[John Simms]

Hi All,
I would use normal mode analysis to study rhodopsin, which is a membrane
protein.
I have tried to EM the protein, in a vacuum, using cg in double precision,
but cant get the Fmax
to a level useful for NM analysis. The minimization stops at about Fmax ~
30, and what ever i try
i cant get a level lower than this. Has anyone used NM on membrane proteins,
any sucess?
As usual any help will be gratefully accepted.
Cheers
John