[gmx-users] LJ-14 energy

Thu Jul 16 21:21:41 CEST 2015

On Thu, Jul 16, 2015 at 1:24 PM Ming Tang <m21.tang at qut.edu.au> wrote:

> Dear Justin,
>
> Thanks.
> 1.  The total Lennar-Jones 12-6 energy of the whole system is the addition
> of LJ-14, LJ-SR and LJ-LR. Analogously, the coulomb energy is the addition
> of coulomb-14, coulomb-SR and coulomb-LR. Is my understanding of your
> explanation right? Besides, in Gromacs, is the potential energy the
> addition of G96Bond, G96Angle, Proper-Dih, Improper-Dih, LJ-14, Coulomb-14,
> LJ-SR, LJ-LR, Coulomb-SR and Coulomb-LR?
> You are right. That's why I don't get the LJ-LR and Coulomb-LR options
> when using g_energy. Suddenly, I realised that my understanding of the
> twin-range approach was totally wrong. For cutoff-scheme = verlet, rlist
> cannot be smaller than rvdw = rcoulomb, and When using twin-range method,
> either coulombtype = cut-off with
> rcoulomb ≥ rlist or vdwtype = cut-off with rvdw ≥ rlist. Does this mean
> that for twin-range approach, rlist = rcoulomb = rvdw when cutoff-scheme =
> verlet? However, even if I set vdw-modifier = potential- switch, the
> rlistlong larger than rlist is reset to be equal to rlist by gromacs, and
> there is not LJ-SR option when using g_energy. I am totally lost. Can you
> help to tell me how does twin-range work when cutoff-scheme = verlet?
>

http://manual.gromacs.org/documentation/5.1-rc1/user-guide/cutoff-schemes.html
(and equivalent docs for earlier versions) indicate that twin-range is not
supported by the Verlet scheme.

(Technically, it could be supported, and some forms of it are in fact used
by the PME-tuning facility, but some of us are unconvinced of the technical
merit of such forms, nor do we like the confusion created by how such
group-scheme features are named and implemented in GROMACS. So, if there is
ever support, it's likely to be from a clean slate, and after we remove the
group scheme.)

Another question is I used the following code to make my cut-off parameters
> be consistent with those used for the triple-range cut-off scheme in the
> paper defining Gromos 54a7 force field:
>
> coulombtype      =  reaction-field
> coulomb-modifier =  potential-shift
> rcoulomb-switch  =  0.8
> rcoulomb         =  1.4
> epsilon_rf       =  61
>
> Currently, I think it is wrong. It seems that rlist = 0.8 is reasonable.
> But rlist should not be smaller than rcoulomb when cutoff-scheme = verlet.
> How to achieve this triple-range cut-off scheme?
>

You can't.

Mark

> 2.   The pull rate I use is 4e-5/ps. I thought it is small so that the
> energy of water can be treated as constant during the pull process. I
> forgot to consider the water-protein interaction and that my pull rate is
> much larger than the pull rates used in the experiments which is in order
> of micrometre per second and is much more relevant to physiological pulling
> rate. You are right, I cannot treat the trends of the system's energy as
> those of the protein's energy. But how can I get the energy of the protein?
> Is it feasible to set all the atoms of the protein as one energy group, and
> do rerun to achieve this?
>
> Thanks,
> Regards
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin
> Lemkul
> Sent: Thursday, 16 July 2015 11:20 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] LJ-14 energy
>
>
>
> On 7/15/15 8:39 PM, Ming Tang wrote:
> > Dear Chaban and Justin,
> >
> >
> >
> > Sorry for the mis-action. Please ignore my last email.
> >
> >
> >
> > Thank you both for your free help.
> >
> > I am pulling a collagen triple helix in a periodic water box using
> > umbrella direction-periodic. I want to calculate the Lennard-Jones
> > 12-6 of the protein. According to Gromacs manual, it contains
> > repulsive short-range term and attractive long-range term. Is the
> > Lennard-Jones 12-6 energy simply the addition of LJ-SR and LJ-LR? I am
> > interested in the energy trends more than
>
> LJ-LR only exists with a twin-range cutoff approach.  The total LJ between
> any groups also includes LJ-14 for intramolecular terms.  Intermolecular LJ
> would be the sum of LJ-SR and LJ-LR, if the latter exists.
>
> > the energy absolute values. So, if I can calculate the LJ 12-6 of the
> > whole system, it is fine, because I can assume the energy of the water
> > is not subject to change due to pulling.
> >
>
> Why can you assume that?  You're pulling a structure, which is a
> non-equilibrium process.  There will be different interactions as a
> function of time.
> Water-water interactions at long distance from the protein indeed are
> unlikely to be affected, but those close to the protein may be different
> (though electrostatics/hydrogen bonding are probably much more interesting).
> Water-protein interactions certainly can't be assumed to be unchanging
> during pulling.
>
> -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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