RE: Umbrella sampling of a protein through a membrane

From: Villalain Boullon, Jose (jvillalain_at_umh.es)
Date: Fri Apr 12 2019 - 01:40:34 CDT

Dear Victor,

Thank you very much for your response. In principle I would like to use ABF. About the overlap between adjacent windows, does it means that I have to use overlapping windows ?. If the width of the window is 2 A, as I have read in other papers, which is then the overlap ?. Or it means that the overlap is 2 A, whatever the window range I use?.

Thanks a lot.
José


De: Victor Kwan <vkwan8_at_uwo.ca>
Enviado el: viernes, 12 de abril de 2019 6:05
Para: namd-l_at_ks.uiuc.edu; Villalain Boullon, Jose <jvillalain_at_umh.es>
Asunto: Re: namd-l: Umbrella sampling of a protein through a membrane

Hello,

Do you want to do ABF or US?

DistanceZ uses center of mass of the atom group. Whether or not it is a suitable RC depends on the protein itself.

On the width of US (to a lesser extent, ABF) simulations: You want sufficient overlap between adjacent windows. That is, again, system dependent.

Cheers,

Victor

On Thu., Apr. 11, 2019, 3:01 a.m. Villalain Boullon, Jose, <jvillalain_at_umh.es<mailto:jvillalain_at_umh.es>> wrote:
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





x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x
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)
x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x

On Thu., Apr. 11, 2019, 3:01 a.m. Villalain Boullon, Jose, <jvillalain_at_umh.es<mailto:jvillalain_at_umh.es>> wrote:
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





x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x
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)
x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x

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