membrane surface tension

You successfully prepared your system. Now: How do I tell Hippo to produce a trajectory from it? What parameters to choose? And what should I do when things go wrong.
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jsimms
Posts: 3
Joined: Sun Aug 30, 2009 5:49 am

membrane surface tension

Post by jsimms » Wed Jun 08, 2011 1:03 pm

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
Developer
Posts: 38
Joined: Sun Jun 15, 2008 10:27 pm

Re: membrane surface tension

Post by martin » Sun Jun 12, 2011 12:30 pm

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

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