[gmx-users] gromacs rerun calculate the energy

[Mark Abraham]

Hi,

You can't get an estimate including the long-range interaction by using a
short-ranged method. If the long range matters, it'll be wrong and if it
doesn't, you won't know that.

Mark

On Tue, 1 Aug 2017 22:43 Varvdekar Bhagyesh Rajendra <
bhagyesh.varvdekar at research.iiit.ac.in> wrote:

> 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,
>
> Bhagyesh
>
> ----- 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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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