g_remove_water

Takes a gro file containing a bilayer and remove any water molecules inside the bilayer.

To remove molecules, it's based on Z mean of the upper and lower leaflet.

At the end, the residues and the atoms are re-numbered and the number of atoms at the 2nd line is updated. Title and box vectors are kept.

The atom to determine the upper and lower leaflet (typically the phosphate) can be set with the lipid_atom option (default = P1)

The atom to determine the water molecule can be set with --water_atom option. For all-atoms files, you have to use the oxygen atom as a reference.

Water molecules can also be removed if they are in a sphere centered on the geometrical center of the atom with a given set of residue name. Use --sphere to set the list of residue names to use for the center calculation and --radius to set the radius of the sphere.

Usage

g_remove_water.py -f coord.gro [options]

The programs require an inpute file (-f option) in a GRO file format. It writes the output in a GRO file with a default name out.gro. It can be change with the -o option.

Options

-f FILE:

The input file (.gro)

-o FILE:

The Output file (.gro)

--lipid_atom:

The reference atom for the bilayer (P1 by default)

--water_atom:

The reference atom for the water. Use the oxygen. (OW by default)

--sphere:

Remove water molecules if they are in a sphere centered on the geometric center of atoms with the given residue names. You need the --radius option to be filled. Multiple resnames can be given.

--radius:

Remove water molecules if they are in a sphere of this radius centered on a given set of residue names. You need the --sphere option to be set.

Run tests

Unit tests are available for g_remove_water in test_g_remove_water.py. You can run them by simply execute test_g_remove_water.py:

python test_g_remove_water.py

The nosetests python module allows a smarter display of the report by displaying test function outputs only when the test fail. If you have nosetests installed you can run the test by typing:

nostests test_g_remove_water.py

Licence

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

A copy of the GNU General Public License is available at http://www.gnu.org/licenses/gpl-3.0.html.