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

[abdullah ahmed]

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.
> 
> -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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