[gmx-users] Removal of Waters in Hydrophobic Core

[Justin Lemkul]

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

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

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