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

Justin A. Lemkul jalemkul at vt.edu
Tue May 4 14:41:15 CEST 2010

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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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