query for system size in pmf calculation

From: Atanu Maity (atanuchem48_at_gmail.com)
Date: Fri Nov 20 2015 - 05:24:47 CST

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

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