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

[abdullah ahmed]

 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. 

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.  

> 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
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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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