[gmx-users] Removal of Waters in Hydrophobic Core
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.
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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