From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
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,
though.
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
anyway;
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
time.
Giacomo
On Fri, Nov 20, 2015 at 6:24 AM, Atanu Maity <atanuchem48_at_gmail.com> 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
> NAMD.
>
> 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 http://goo.gl/Q3TBQU http://giacomofiorin.github.io/ https://icms.cst.temple.edu/members.html
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