[gmx-users] inter- and intra-molecular hbond analysis

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Sat Jan 20 01:16:16 CET 2018

Dear Gromacs users,

Given a mixed bilayer composed of two lipids (type A and B), I would like
to calculate:

1) "Intramolecular" h-bonds for a lipid type to see if part of lipid (NH3+
of PE) is interacting with some other part of itself (PO4- of the same

2) "intermolecular" hbonds between A-A, A-B, and B-B.

If I understood correctly, gmx hbond does not distinguish between the
inter- and intra-molecular hbonds. So, choosing A and A lipids will give
both the intramolecular and intermolecular hbonds between lipids type A in
the system.

One solution could be doing this analysis on each individual lipid of type
A first, and then make an average over all the lipid type A in the system.
This will give the intramolecular hbonds (lets call it H-intra)

Next, calculating the hbonds between lipid A and A as gmx hbond does by
defualt. This will give both intermolecular and intramolecular
hbonds between A lipids in the system (Lets call it H-Both).
Thus, (H-both) - (H-intra) = (H-intermolecular hbond between lipids of the
same type)

I think there should be an easier way to do this (especially H-intra) and I
do not know.
I was wondering if anyone has any suggestion?

This is the same problem I am facing when I want to calculate the min-dist
between two groups, i.e. the intermolecular and intramolecular min-distance
between two groups of atoms.

Thanks in advance for your comments,

*Rewards work better than punishment ...*

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