On 5/05/2010 12:27 AM, 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.
Affected? Yes. Significantly affected? Probably not. The magnitude and
variance of the water-water Coulombic interaction can drown it. It's
analogous to the observation that in order to recognise that a single
person is waving at someone else in a busy crowd, you've got to watch
for a while.
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.
There is no meaningful single energy value. This is not gas-phase
quantum chemistry. You need to sample an ensemble in order to have the
ability to average out the solvent (and solute!) degrees of freedom. See
http://en.wikipedia.org/wiki/Free_energy_perturbation for example.
Mark
> 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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> > >
> > > --
> > > ========================================
> > >
> > > 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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