[gmx-users] settingparameters for energy minimization

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 2 13:31:18 CET 2009

vivek sharma wrote:
> Hi There,
> I am trying to do energy minimization of some protein molecule, and I 
> have following queries for the same.
> 1. Can I define some RMSD tolerance, such that RMSD value of the 
> molecule during the energy minimization will not vary more than some 
> predefined value.

No, nor would it do much good.  Do you expect the RMSD to change much during EM? 
  I usually see an RMSD no greater than 0.2 Ang.

> 2. Which integrator is better to use SD or CG ?

That depends on your definition of "better."  Try both and see which results you 
think are more reliable, otherwise consult some textbook material or literature 
references on the algorithms.

> 3. what algorithm should be used for  long-range electrostatic 
> interaction PME or cut-off.

PME is more accurate than cut-off.


> Please suggest for the above queries.
> 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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