[Chimera-users] Regarding Structure minimize

[Elaine Meng]

Hello,
There is no single answer to this question.  You have to use your own judgment because it depends completely on the specific details of the starting structure and how many problems it might have. It also depends what you want to do with the ending structure.  Also you should understand there is limited ability of minimization to "fix" any problems with a structure, since it will just go the nearest local minimum, which might still be a poor structure.  

To learn more about this subject there are probably many textbooks on computational chemistry and structure of molecules.

Interval is only how often the changes are displayed, and does not have any effect on the final result.  

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Mar 7, 2020, at 1:30 PM, Yash Bahl <yashbahl1999 at gmail.com> wrote:
> 
> To do structure minmization, what is the adequate values? 
> Steepest descent should be changed to 75 from 100. 
> What else?
>  Should intervals be also changed to 25?
> Thanks 
> _