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

[Lara Bunte]

Hello

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. 


My thoughts:


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
Greetings
Lara