[gmx-users] File editing - only one layer of water around a molecule (again)
lara.bunte at yahoo.de
Tue May 1 19:55:59 CEST 2012
After I understand how to select a
molecule with water layers out of a molecule in a box filled with water
(again thanks to Justin and Mark for lots of help), I want to
understand more about choosing good parameters in g_select.
I have the command
g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 of resname ISO'
ISO is my molecule and SOL the water around it. The number 0.5 means, that this is the distance in nanometers. Now I asked myself what number I should use for just keeping three layers of water.
The dilation of a water molecule is 0.28 nm and the bond leght of a O-H bond is 0.096 nm, hence the number in g_select should be
3 * (0.28 + 0.096) nm = 1.128 nm
So the command for GROMACS should be
g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within 1.128 of resname ISO'
Are this thoughts chemical correct?
Thanks for helping me
More information about the gromacs.org_gmx-users