[lammps-users] HBond computation

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1

Dear Lammps Users, I ran simulations using, among all settings*, pair_style lj/cut/coul/long 12.0 9.0* and GROMOS54A7 as force field. All pair_coeff were stored in a different file.

Once completed, I studied the trajectories and I noticed the generation of hydrogen bonds throughout the simulations (mainly looking at the donor-acceptor atoms distance).

I was wondering if there was a way to calculate the energy and strength of the HBs that are formed during the simulations.

Reading the manual, I found the command:

pair_style hbond/dreiding/lj or hbond/dreiding/morse

and I also read that with the pair_style hybrid/overlay command I can use this style together with the one I used for my simulations.

But it’s unclear to me how can I combine the pair_coeff commands for both styles.

Thank you very much in advance for your help.

Best Regards,

Dott. Nicola Gambacorta

PhD Student

Mail: [email protected]

Dipartimento di Farmacia-Scienze del Farmaco

Università degli Studi di Bari "Aldo Moro”

Via Orabona 4, 70125 Bari (Italy)

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two things.

a) you don’t want to add any of the hbond pair styles to your simulation directly, since that would modify your model and add explicit hydrogen bond terms taken from the dreiding force field.
so adding those would invalidate your model and produce bogus results. quantifying hydrogen bond energy contributions is a difficult thing since they are usually not explicitly added to the force field but a consequence of the balance of the coulomb and lennard-jones interactions and the geometry of the model. in general, you want to do this as in independent computation and it will be based on some heuristics. there should be a large number of publications on this topic with people arguing over what is the best way to identify, count and quantify the hydrogen bond interactions. those papers should give you an idea what you might want to do.

b) how the pair_coeff commands are different for hybrid pair styles versus normal setups is discussed at great length in the documentation for the hybrid pair styles.

axel.