[gmx-users] Doubt in Energy minimization and Position restrained

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 9 12:11:45 CEST 2008

vivek sharma wrote:
> Hi there,
> My apologies for asking question from basics.
> I have one doubt regarding order of Position restrained and Energy 
> minimization. While running Position restrained, it soaks water molecule 
> well within the protein molecule. In doing so on rearranging atoms it 
> will again raise the energy of system (if I am not wrong). So, do we 
> need to run Energy minimization again ?

PR equilibration may or may not raise the energy.  There is a pretty good chance 
that soaking in the solvent will establish more favorable water orientation 
(hydrogen bonding), thus potentially lowering the energy.

There is no need to re-run EM after doing PR.  Minimization simply provides a 
reasonable energetic starting point for the simulation, to avoid major steric 
clashes and unreasonable forces.

Just because potential energy rises, doesn't mean the behavior is unreasonable.


> If not, then why ?
> With Thanks,
> Vivek
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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