[gmx-users] g_rdf and lipid bilayer hydration

Ioannis Beis ibeis at mail.student.oulu.fi
Mon Feb 6 15:26:37 CET 2012

Dear Gromacs users,

I have a question related to the use of g_rdf for the calculation of  
hydration of a lipid bilayer patch. I used g_rdf with -surf flag (I  
tried both mol and res) and two index groups: the oxygens of waters as  
first group and the atoms of the headgroups as second group. I used  
the above hoping to calculate the distribution of water molecules  
around lipid headgroups with the distance calculated from the closest  
headgroup atom to each water and counted only once. The resulting  
graph does not have the two large and one small hydration peaks  
followed by the plateau as expected, but instead has two tiny peaks  
and then behaves as increasing function with distance. The hydration  
profile of the polar components of the bilayer alltogether is almost  
identical to the hydration of a single lipid that I calculated in a  
similar manner, which doesn't make sense to me.

In addition to that, the number of oxygens in each one of the 1500  
bins (I used the default number of bins) is in average around 1000,  
while the number of water molecules in my system is only 6070. This  
means that somehow there exists a "degeneracy" in the calculation of  

Is it possible that the problem is correlated to the lack of normalization?

So what does g_rdf calculate in my case? Is there a way with or  
without g_rdf to obtain the hydration profile, as well as integration  
of the latter up to a distance that I could subsequently decide based  
on the results?

Thank you in advance.

Best regards,

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