membrane surface tension

[jsimms]

Hi,
I have a 7 isolated transmembrane helices from a GPCR (b2ar). I just want to have a look at how the structure of the TM changes between isolated helices and the packed complete structure. Two helices (tm2 and tm6) dont stay in the "bilayer" region very long and float into the bulk solvent and i would like to restrain the helices to the confines of the bilayer. I know this isnt very physical, but i just want to have a look. I was wondering whether increasing the sigma_membrane would help. Also if i change sigma_membrane do i need to alter sigma for membrane simulations.
any help would be awesome
cheers
john

[martin]

Hi,

Yes, the best option is to increase sigma_membrane. In essence that will increase the hydrophobicity of the bilayer. If you still have problems you can try restraints, will dig it out for you if you need.

Good luck!
Martin