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

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 5 16:09:49 CEST 2010 

On 5/05/2010 11:44 PM, abdullah ahmed wrote:
> 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?

If you don't use genbox, you don't get water added.

This is probably a really good time to go and do some tutorial material 
and some background reading. :-)

Mark

> 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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>  > > > --
>  > > > ========================================
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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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