[AMBER] Sampling of membrane-protein system

From: Ofir Tal <pantufel.hotmail.com>
Date: Wed, 11 Nov 2015 11:13:21 +0000

Dear members,


I simulate large system (~250 thousand atoms) of membrane protein dimer embedded inside a POPC membrane on 2X gtx980 GPUs.
The system and its variant ran 200ns. The systems are stable in terms of energy and area-pre-lipid. RMSD seems to keep constantly raising along the simulation, although less in comparison with the first 50ns. RMSD increased by ~1A during the last 150ns.
I want to enhance the systems sampling sufficiently, so I think it need to be sampled in one of the methods - aMD or umbrella.

Which of the methods would be the best choice for sampling a big membrane system?

Is it possible or sufficient to run the simulations in triplicates with different random seeds (200ns each) instead?


As I understand from the literature, MMPBSA.py in general is not suitable for membrane systems. Is it possible to calculate binding energy values (of the membrane complex) using just the 'Decomposition' method of MMPBSA, directed to the interaction area of the two sub-units (only between residues which participate the interaction of sub-unit-A and sub-unit-B)?


Your reply is greatly appreciated.

Thank you,

Ofir Tal, PhD
Structural Bioinformatics
Bioinformatics Knowledge Unit - BKU
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Received on Wed Nov 11 2015 - 03:30:05 PST
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