[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.
Mark
>
> 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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