[gmx-users] LJ-14 energy

Sat Jul 18 21:57:00 CEST 2015

If their paper doesn't explain their method well enough for you to
reproduce it, please ask them! :-)

Mark

On Sat, 18 Jul 2015 12:26 Ming Tang <m21.tang at qut.edu.au> wrote:

> Dear Mark,
>
> Thanks for your link. Now I have a better understanding on cutoff-scheme =
> verlet. This also let me notice that there are difference between version
> 5.0.4 and the earlier versions. Actually I came across another simulation
> problem, which made me feel confused for a long time. I saw several
> publications, in which people restrained the COM of one group (referred as
> reference group) in SMD with version 4.6, but I did not find the way to
> achieve this. both freezing group and restraining all the atoms in the
> group fix the atoms not COM. Do you have any suggestion for me?
>
> Thanks.
>
> -----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 Mark
> Abraham
> Sent: Friday, 17 July 2015 5:21 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] LJ-14 energy
>
> 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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