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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jan 30 13:12:46 CET 2012

On 30/01/2012 10:44 PM, Ioannis Beis wrote:
> 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.

You can have either the distribution over time of the minimum distance 
between any water oxygen and any lipid headgroup atom from g_mindist, or 
the distribution over space of water oxygen atoms around lipid headgroup 
atoms (a.k.a. radial distribution function) from g_rdf. The above does 
not make clear to me that you are clear about which one you want.

> 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.

Yep. That's what g_mindist does. I think you want g_rdf.


> 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!
> Ioannis

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