[gmx-users] How to proceed with energy minimization for Normal Mode Analysis

[David van der Spoel]

Anirban Ghosh wrote:
> Hi,
> I am new to GROMACS. I want to perform Normal Mode Analysis of a 
> protein. For that I require a well minimized structure. I have minimized 
> my structure using steepest descent and conjugate gradient. But the 
> structure seems to have got struct in a local energy minima. How should 
> I proceed to get a well minimized structure in order to go for Normal 
> mode Analysis?
> Please suggest any protocol.

you are asking us to solve the global minimization problem for a high 
dimensional system. sorry. such algorithms do not exist.

you could try to do MD and then minimize structures along the 
trajectory, do NM on all of them and compare the results. much better 
statistics.
> 
> Regards,
> 
> 
>  
> *Anirban Ghosh*
> *M.Tech Bioinformatics*
> *University of Hyderabad*
> *Hyderabad - 500 046*
> *Andhra Pradesh*
> *India*
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se