[gmx-users] electro-static potential energy after minimization

[Mark Abraham]

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: 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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