[gmx-users] Steered MD simulation

James Starlight jmsstarlight at gmail.com
Sat Feb 4 19:35:26 CET 2012

Dear Gromacs Users!

I'm investigating activation of the GPCRs receptor in the membrane
Because of potentialy long time required for the activation of such
receptors I want to perform some sort of steered MD simulation. For example
I I want to change rotameric dihedrals of some important swith residues
during the productiv MD run to simulate destabilisation of some cruisial
interactions wich stabilise innactive conformation of the receptor.

some example of such simulation without required detailes could be found

Could you provide me with the simlest example of methodology of such
dihdral changes during simulation as well as application of some external
forces on the specified objects?

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