[Chimera-users] Energy Minimization

Elaine Meng meng at cgl.ucsf.edu
Thu May 13 11:17:07 PDT 2010

Hi Monisha,
Look in the Reply Log (under Favorites in the Chimera menu).  It gives  
total energy at start and updates every N steps (default 10),  
something like:

Initial energy: -1629.083349
Step 10
Potential energy: -2049.858439, Gradient norm: 743.655395
Updated 696 atoms.  RMSD: 0.025894
Finished 10 of 100 minimization steps
Step 10
Potential energy: -2283.142562, Gradient norm: 350.044125
Updated 696 atoms.  RMSD: 0.014307
Finished 20 of 100 minimization steps
(... etc. ...)

However, it does not break down the energy into different parts  
(electrostatic, VDW, ...), you can only get the total.
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 13, 2010, at 11:10 AM, Eric Pettersen wrote:
> Dear All,
> Using Minimize command, I can minimize the the energy of the  
> protein. But is
> there a way by which I can check the energy the protein before I  
> perform the
> minimization and after minimization or least after minimization.
> Thanks and Regards
> Monisha
> (originally sent to chimera-bugs)
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