[gmx-users] GPCR/any protein modelling

[Chris Shaw]

Hello All, 

I am attempting to model a GPCR based on the recently reported crystal structure of rhodopsin. I have done this and are now trying to do some MD on this model. This is where it goes wrong. I have tried to do some MD run on the model as with the "Getting started tutorial". Short runs in water i.e. 50 ps all is fine, however during longer runs i.e. 500 ps (again in water) the secondary structure of the model degrades greatly. Could anyone help me as to where I am going wrong. ANY HELP WOULD BE GREATLY APPRECIATED!!!!

Cheers

Chris




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