[gmx-developers] Discrepancy with LAMMPS in Coulomb (SR) Coul. recip. energy

Michael R Shirts Michael.Shirts at Colorado.EDU
Thu Oct 24 18:20:28 CEST 2019

I’d also check out https://link.springer.com/article/10.1007/s10822-016-9977-1 for how to compare energy outputs of different simulation programs (including GROMACS and LAMMPS).

Michael Shirts
Associate Professor
michael.shirts at colorado.edu<mailto:michael.shirts at colorado.edu>
Phone: (303) 735-7860
Office: JSCBB C123
Department of Chemical and Biological Engineering
University of Colorado Boulder

From: <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> on behalf of Berk Hess <hess at kth.se>
Reply-To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
Date: Wednesday, October 23, 2019 at 11:14 PM
To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
Subject: Re: [gmx-developers] Discrepancy with LAMMPS in Coulomb (SR) Coul. recip. energy


This is a question for the gmx-users list, but I'll answer here.

In general decomposition of Coulomb PME terms is meaningless, because there is no unique definition of the components. Also you need to have all parameters identical. Having said that, I think the main difference is because GROMACS adds the self correction to the real space term and LAMMPS seems to add it to the the reciprocal space.



On Oct 24, 2019 00:11, Jeet Majumdar <mail2majumdar at gmail.com> wrote:
Dear all,
I was running a simulation with bulk water and CNT, with the protocol -> Minimization, NPT, NVT. Keeping as much close as possible, I did the same simulation in LAMMPS too. I observe that the LAMMPS and GROMACS log file shows complete disagreement in sign and value in the coulomb energy calculation in real space and reciprocal space; in all the steps. Although upon adding the two parts (real+reciprocal) to get total Coulomb energy, they are matching within error limit. Can anyone please explain me why am i getting such a weird result? Is it some in-build difference in calculation technique, or am I going wrong somewhere? I couldn't figure it out.

GROMACS: (in kJ/mol)

Coulomb (SR) Coul. recip.
 -3.59079e+05 8.41910e+02

in kcal/mol this translates to
Potential Kinetic En. Total Energy Temperature Pres. DC
-85821.94072 201.221319

LAMMPS: (in kcal/mol)

E_coul = 177903.2534 E_long = -270193.3273

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