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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Department of Biochemistry
Virginia Tech
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