[gmx-users] electro-static potential energy after minimization
Justin A. Lemkul
jalemkul at vt.edu
Tue May 4 17:38:45 CEST 2010
abdullah ahmed wrote:
> The charged residues are on the inside of the structure, and so are not
> affected by the solvent. There are also no other charged residues in the
> structure. Furthermore, the structure is quite small 22 (residues). So I
> am still tempted to say that the coloumbic energy of the system should
> be affected by these charges.
>
Certainly. The total Coulombic energy is affected by any charge interaction in
the system. I am not trying to imply that there is a solvent-dependence on your
residues interacting. What I am saying is that, for most systems, the majority
of the atoms in the system are water, so the largest contributor to the total
Coulombic energy is intra-solvent interactions, which aren't of interest to you.
So by looking at the total of Coulombic terms, you are masking a more subtle
effect with a crude metric. The interaction between your two residues is what
you really want to measure. If you have a total Coul. (SR) on the order of
10,000 kJ/mol (for the system) and you alter that figure by even 50 kJ/mol, is
that a meaningful change? That's why it's hard to determine how meaningful your
results are in the absence of any true simulation.
> Regarding MD, the structure I am using is already in an optimal
> position. I am not particularly interested in refining the structure.
> All I really need is the energy value.
>
Yes, but if that interaction is meaningful, it should persist during MD :)
-Justin
> > Date: Tue, 4 May 2010 08:53:48 -0400
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] electro-static potential energy after
> minimization
> >
> >
> >
> > abdullah ahmed wrote:
> > > Thank you for your reply,
> > >
> > > However, I can not use MD.
> > > I would simply like to ask whether I am correct in assuming that the
> > > minimized energies of the two structures should be very different.
> > >
> >
> > What exactly are you measuring? The Coulombic energy of the system?
> If so,
> > that term is going to be largely controlled by the solvent and thus
> you will see
> > little, if any, difference at all between the two systems. If you're
> measuring
> > the Coulombic energy between two residues, yes, you should see a
> clear difference.
> >
> > I don't understand your argument against MD. To me, restrained
> minimization
> > doesn't tell you much at all. But maybe I don't fully grasp your
> intentions for
> > these calculations.
> >
> > -Justin
> >
> > > > Date: Tue, 4 May 2010 08:41:15 -0400
> > > > From: jalemkul at vt.edu
> > > > To: gmx-users at gromacs.org
> > > > Subject: Re: [gmx-users] electro-static potential energy after
> > > minimization
> > > >
> > > >
> > > >
> > > > abdullah ahmed wrote:
> > > > > Hello everyone,
> > > > >
> > > > > I have two protein structures, and the insides of both are not
> exposed
> > > > > to water.
> > > > > One structure contains two oppositely charges residues (GLU and
> LYS)
> > > > > facing each other. The second structure contains a GLU residue
> only.
> > > > > Upon minimization I had expected the coloumb energies of the first
> > > > > structure to be lower than that of the second. However, this was
> > > not the
> > > > > case, they are both very similar.
> > > > > Does anyone have an idea as to why this has happened?
> > > > > (The only explaination I can come up with is that perhaps the
> > > effect is
> > > > > so small that it can not be seen)
> > > > >
> > > >
> > > > We discussed this at length yesterday. By doing a simple energy
> > > minimization
> > > > (in which, if I recall, you are applying position restraints), you
> > > stand to
> > > > prove very little. By doing MD and obtaining an ensemble of
> energies,
> > > you stand
> > > > a better chance of calculating a relevant energy.
> > > >
> > > > > I was not sure if providing PDB and .mdp files would be
> helpful, but I
> > > > > can send then in my next mail if neccesary.
> > > > >
> > > >
> > > > The .pdb file is unnecessary. Only post the .mdp file if it has
> > > changed since
> > > > the one you posted yesterday.
> > > >
> > > > -Justin
> > > >
> > > > > Thank you in advance!
> > > > > Abdullah Ahmed
> > > > >
> > > > >
> > >
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> > > >
> > > > --
> > > > ========================================
> > > >
> > > > Justin A. Lemkul
> > > > Ph.D. Candidate
> > > > ICTAS Doctoral Scholar
> > > > MILES-IGERT Trainee
> > > > Department of Biochemistry
> > > > Virginia Tech
> > > > Blacksburg, VA
> > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > >
> > > > ========================================
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> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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