[gmx-users] Interaction energy

rose rahmani rose.rhmn93 at gmail.com
Sat Jan 5 10:09:12 CET 2019


How can i find these information about charmm forcefield? Would you please
help me?

On Tue, 27 Nov 2018, 00:22 Mark Abraham <mark.j.abraham at gmail.com wrote:

> Hi,
>
> On Mon, Nov 26, 2018 at 7:47 PM Nick Johans <johans.nick93 at gmail.com>
> wrote:
>
> > On Mon, 26 Nov 2018, 21:28 Justin Lemkul <jalemkul at vt.edu wrote:
> >
> > >
> > >
> > > On 11/26/18 10:51 AM, Nick Johans wrote:
> > > > On Mon, 26 Nov 2018, 18:22 Justin Lemkul <jalemkul at vt.edu wrote:
> > > >
> > > >>
> > > >> On 11/22/18 11:41 AM, Nick Johans wrote:
> > > >>> Hi
> > > >>>
> > > >>> I am beginner in MD. Maybe it is not a wise question but i want to
> > > >>> calculate the interaction energy between protein and ligand and
> also
> > > PMF
> > > >> in
> > > >>> different distances. But i don't know what is the didference
> between
> > > >> PMF, i
> > > >>> mean free energy in particular(by umbrella sampling) and the
> > > interaction
> > > >>> energy (by g_energy tool) in my case?
> > > >> Interaction energy is a pairwise decomposition of short-range
> > nonbonded
> > > >> interaction energy in the system. This energy is usually not
> > physically
> > > >> meaningful, but if the force field has been parametrized in such a
> way
> > > >> that it is, the interaction energy is a contribution to the enthalpy
> > of
> > > >> the system.
> > > >>
> > > > What forcefields embedded in GROMACS do, yes?
> > >
> > > AFAIK only CHARMM.
> > >
> > Interesting! You mean interaction energy calculated by for example AMBER
> > may not be true? Why?? What makes CHARMM unique??
> >
>
> As Justin said, the difference is in the way it is parametrized.
> Forcefields are generally built to be additive, but it does not follow that
> they are decomposable.
>
> > > If coulomb energy is also existed between pairs, so the interaction
> > > energy
> > > > will be LJ+Coulomb yes?
> > >
> > > Pairs are 1-4 (intramolecular) interactions, so if you define
> > > interaction energy between two nonbonded species, you'll get zeroes for
> > > all the pair energies, by definition.
> > >
> > It's exactly the SR(short range) selection in g_energy, yes?
>
>
> You seem to be using a looser definition of pairs than is usual in
> discussion of GROMACS topologies.
>
>
> > all long range
> > are zero.
>
>
> If there's a long-range model, then such interactions are not uniformly of
> zero magnitude...
>
>
> > But coulomb and LJ are non-zero. So, in this case the interaction
> > energy would be
> > Short range LJ+ Short range Coulomb , true?
> >
>
> As far as I'm concerned, you can invent whatever quantity you want, but the
> burden is on you to demonstrate that there's a reason to connect it to
> something physical.
>
> Mark
>
>
> > >
> > > > So what about PMF. It seems like an interaction energy too, but more
> > > > accurate one???
> > >
> > > That's not what a PMF is. A PMF is the change in free energy of a
> system
> > > as a function of progress along a reaction coordinate.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Office: 301 Fralin Hall
> > > Lab: 303 Engel Hall
> > >
> > > Virginia Tech Department of Biochemistry
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalemkul at vt.edu | (540) 231-3129
> > > http://www.thelemkullab.com
> > >
> > > ==================================================
> > >
> > > --
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