[gmx-users] electro-static potential energy after minimization
abdullah_renk_ahmed at hotmail.com
Tue May 4 14:50:21 CEST 2010
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.
> 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.
> > 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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