Re: query for system size in pmf calculation

From: Giacomo Fiorin (
Date: Fri Nov 20 2015 - 08:52:35 CST

Hello Atanu and Souvik, in principle you can change the dimensions of the
water layer for as long as they do not affect the PMF. If the peptide has
some charged residues or zwitterionic termini, I wouldn't recommend that,

Notice in general for peptide-membrane insertions that:
a) you need a large bilayer to accommodate the changes in area per lipid,
and the cost associated to compression of the lipids is non-negligible
b) you are looking into a rather complex process, for which a single
collective variable may not be enough and you may need a very long sampling


On Fri, Nov 20, 2015 at 6:24 AM, Atanu Maity <> wrote:

> Dear Users,
> We are trying to get the pmf for membrane insertion of a peptide. For that
> we have used the distance between centre of mass of the protein and the
> lipid as reaction coordinate and use ABF module with collective variable of
> Should we keep the water-layer length same for all of the windows or we
> can tune it according to the position of the peptide along the reaction
> coordinate ?
> With regards,
> Atanu Maity
> Research Scholar
> Bioinformatics Center
> Bose Institute, Kolkata

Giacomo Fiorin
Assistant Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213

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