[AMBER] free energy profile

From: Lars Skjærven <lars.skjarven.biomed.uib.no>
Date: Tue, 8 Jun 2010 21:47:49 +0200

Dear amber users,

Given two long MD simulations (NVE) of the same protein that sample
two different conformational spaces (e.g. an opening vs a more fixed
conformation due to nucleotide binding), would it be possible to
calculate a free energy profile that can be related to the
conformations in the trajectory?

Is this only possible by performing an umbrella sampling, or would it
make sense to extract internal energies and solvation terms and relate
this to the conformational changes somehow?

In regard to umbrella sampling, would it be reasonable to perform it
to drive large scale conformational changes? i.e. by driving an
opening of the protein (300? residues) based on angle/distance
restraints on the structure (where the restraints are set between
center of masses of two/three domains in the protein). Or should it be
limited to smaller conformational changes, as atom-atom restrains?

Any help are greatly appreciated.

Best regards,
Lars Skjaerven

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Received on Tue Jun 08 2010 - 13:00:04 PDT
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