[gmx-users] How to calculate hydration of lipid headgroups by minimum distance means

Ioannis Beis ibeis at mail.student.oulu.fi
Mon Jan 30 12:44:23 CET 2012

Dear Gromacs users,

I am trying to calculate the hydration of lipid headgroups in a lipid  
bilayer system. More specifically, I would like to find the  
time-averaged distribution of water molecules around lipid headgroups  
by means of the closest distance of the water oxygen from any atom of  
any lipid headgroup and plot this distribution as a function of  
distance. I would subsequently like to integrate the number of  
molecules until a distance that I will choose based on the results of  
the first calculation.

g_mindist seems to provide the possibility of doing the latter with -d  
and also allows counting each molecule in the integration only once  
with -group. However, what it can do in the first place is essentially  
different. It calculates the minimum distance among any pair of groups  
of atoms for all times. With -or it calculates the closest distance  
among all frames for every residue. So for my system those would give  
the smallest distance of any water to any headgroup vs time and the  
closest distance of every water with any headgroup among all frames  
respectively. This in practice produces something more than twice the  
van der Waals radius of an atom with small fluctuations.

g_dist doesn't even calculate minimum distances and g_bond isn't relevant.

Is there a way to produce the data I need to use as input for  
g_analyze so that I can eventually get the distribution with a  
combination of conventional Gromacs tools? I would appreciate any  
instructive comment related to my problem.

Thank you very much in advance!


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