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: jalem...@vt.edu
> To: gmx-users@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: jalem...@vt.edu
> > > To: gmx-users@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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> > > --
> > > ========================================
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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
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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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