[lammps-users] Number of hydrogen bonds

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1

Dear LAMMPS users

I want to calculate number of hydrogen bonds in my system. in this system there are an amino acid and some water.
How to do this calculation?

Thanks in advance,
Yasti

2

I don't think this is a built-in capability in LAMMPS, which means you will either have to do this as a post-processing calculation, or write a fix or compute to do this in the code.

--AEI

3

I suggest post process, and not writing a fix. I bet you end up playing around with the H-bond criteria.
Matt

4

Dear LAMMPS users

I want to calculate number of hydrogen bonds in my system. in this system
there are an amino acid and some water.
How to do this calculation?

typically, this is done in post-processing. you have to find
a way to signal the program in question which atom is a
hydrogen bond donor, which a hydrogen bond acceptor,
and which the hydrogen. LAMMPS doesn't know anything
like that from its input.

finally, there are multiple definitions for hydrogen bonds
and you should have a look into the literature which would
be the most appropriate one. typically, a distance and an
angle criterion.

cheers,
    axel.

5

Dear Ahmed, Matt and Axel

Thanks a lot for your help.

Yasti

6

One additional thought. If you can define a H bond by
a distance criterion, then you could possibly use compute coord/atom
with the appropriate O and H atoms in the group. If the
H bond def is more complicated (but still presumably a function
of local geometry), then you could write a compute hbond/atom
command, using compute coord/atom as the template,
and stick in the geometry calc you need to do.

Steve