[gmx-users] File editing - only one layer of water around a molecule

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 4 14:27:40 CEST 2012

On 4/04/2012 7:27 PM, Lara Bunte wrote:
> Hello
> I have a question about editing a pdb file.
> I have a molecule in a box of water as a pdb file. I want to remove all water except of ONE layer around he molecule.  How to do that?
> Do you know a software that is able to do that? Do you know how it could work with programs like PyMol or others?

There's many ways to do it. The GROMACS way is to use g_select with some 
geometric criterion for the layer to generate an index group describing 
the layer, and then using that with trjconv -n to take the subset out of 
the trajectory file.


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