[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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