Umbrella sampling of a protein through a membrane

From: Villalain Boullon, Jose (jvillalain_at_umh.es)
Date: Thu Apr 11 2019 - 02:00:51 CDT

Dear all,

I have been through the NAMD tutorial "Methods for calculating Potentials of Mean Force" and now I would like to obtain the PMF of a peptide through a membrane trying to applied what I think I have learned. I have already minimized and equilibrated the system (protein in the centre of the membrane) and have run SMD on the system through the z direction. So far so good.

I want to obtain now the PMF using ABF but I am standing without really knowing what to do. The coordinate I should use is the z direction and have to select different windows (equally spaced) that cover the entire previous simulation.

The protein changes its structure in a significant way while it passes through the membrane and its centre of mass, relative to the centre of the bilayer, changes significantly through the simulation. I suppose the minimum range of the windows I have to work with should be that one that encompass the entire protein. Am I right ?. But in similar works I have read, the range of the windows is rather small (2 A). Which is really the range I should use ?. Independent of the protein size and/or its centre of mass?.

Thanks a lot for your help.

José

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Prof. José Villalaín
Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE)
Edificio Torregaitán, Ala Este - D2.01
Universidad "Miguel Hernández" - Campus de Elche
E-03202 Elche-Alicante (España-Spain)
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