[gmx-users] Removal of Waters in Hydrophobic Core

Justin Lemkul jalemkul at vt.edu
Sun Feb 25 15:43:35 CET 2018

On 2/22/18 1:33 PM, Smith, Iris wrote:
> Hi Justin,
> In a previous post (Nov 2016) between Chris Neal and Saint Rahman 
> regarding removal of waters in hydrophobic core you mentioned the 
> bilayer_seperator.pl script would be useful in conjunction with gmx traj.
> I am trying to determine the upperz and lowers coordinate values of my 
> bilayer to remove a lot of water in hydrophobic core. How does one 
> determine the z(reference) > z(middle) -> top in the invocation:
> perl bilayer_seperator.pl –in bilayer.gro *–ref 011* *–middle C50* -v

Just define the last carbon in one chain for -middle (as that will 
approximately define the center of the bilayer along the normal) and 
some upper boundary for -ref (in the example, O11 is in the glycerol 
region of DPPC).



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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