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

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Sun Jan 21 22:49:01 CET 2018

```Hi Gromacs users,

I would like to know your opinion on this.

Cheers,
Mohsen

On Fri, Jan 19, 2018 at 5:16 PM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> 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
> lipid).
>
> 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.
>
> Cheers,
> Mohsen
>
>
>
> --
> *Rewards work better than punishment ...*
>

--
*Rewards work better than punishment ...*
```