[gmx-users] electro-static potential energy after minimization
abdullah ahmed
abdullah_renk_ahmed at hotmail.com
Wed May 5 15:44:01 CEST 2010
Thank you for your replies. You guys were right about the problem. The effect of the electrostatic interaction was being masked by the contribution of water to the coulombic energy.
I wanted to ask if there was some way to run minimization or MD in a vacuum? I only started using GROMACS last week and my understanding is limited at the moment. If I understand correctly to do MD or minimization one has to first run the "pdb2gmx", "editconf", "genbox", and "grompp" before being able to run "mdrun." But doing so forces you to add water at the editconf/genbox stage. Is there another way to do this?
Thanks again, and Bonne Journée!
Abdullah
> Date: Wed, 5 May 2010 01:47:29 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] electro-static potential energy after minimization
>
> 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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