[gmx-users] gromacs rerun calculate the energy

Varvdekar Bhagyesh Rajendra bhagyesh.varvdekar at research.iiit.ac.in
Tue Aug 1 22:43:11 CEST 2017

Dear Justin,

To get an estimate of the long range interactions in LIE calculations for protein-ligand binding energy calculations, is it reasonable to change the coulomb type to reaction-field zero instead of changing the rcoulomb from 1.0 nanometre to half of the water box, and the coulombtype from PME to cut-off ? If yes, what should be the rcoulomb with coulombtype = reaction-field zero ?

Also, instead of changing rcoulomb from 1.0 nanometre to half of the water box, does changing it to lets say the box length have better accuracy?

Thank you,


----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Tuesday, August 1, 2017 4:20:54 AM
Subject: Re: [gmx-users] gromacs rerun calculate the energy

On 7/31/17 8:03 AM, 王珍 wrote:
> Hi all,
>        I used Gromacs run the biological system,  which contains water, ions(Na+,Cl-), and nucleic. I used gromacs run the system, and the coulombtype was PME and the cutoff was 10 angstrom,  then I want to use the commond rerun to calculate the interaction of resid 1 and resid 2, I add the energygrps in my mdp, and the coulombtype was PME, the .edr file can be obtained. Then I use g_energy to calculate the coulomb interaction. I have three question.
> first, when the rcoulomb=10 angstrom, and coulombtype=PME, within 10 angstrom, is PME algorithm using ?

Yes, because there are both real-space (within rcoulomb) and Fourier space 
(long-range) terms.

> second, The PME algorithm dived into long range interaction and short range interaction, whereas we only calculate the short range of the coulomb energy using Gromacs, can we obtain the long range of the coulomb energy?

Perhaps by clever use of convert-tpr to zero out charges of certain groups 
(there is a post in the archive from some time ago about this) but I am 
skeptical about the value of such a number.

> Third, when I use rerun to calculate the coulomb energy, the rcoulomb from 1.0 nanometre change to half of the water box I built, and the coulombtype from PME to cut-off, is it reasonable to calculate the coulomb energy?

This is probably the more straightforward way to determine a reasonable estimate 
of the longer-range energy contributions.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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