Mark, 2011/10/26 Mark Abraham <mark.abra...@anu.edu.au>
> > Or that your starting structure is not close enough to a sensible minimum > for a local gradient-based optimizer to do the job. Look at the atoms with > the large forces and see what you can learn. > So for that purpose I've done steep minimization first and only that based on that minimized structure I did CG minimization. I changed the emtool ( from 100 to 1000) as well as step size but my structure always have not been prorely minimized ( based on the system output ). Also I've found that there is third L-BFGS <http://www.gromacs.org/Documentation/Terminology/L-BFGS>algorithm for minimization. In what cases this minimization could be helpfull? > Sorry, we can't make guesses based on things you can't remember details > about. Maybe you want to consider Essential Dynamics. > As I know the Essential dynamics is the type of the PC analysis ( in this case the ensemble of the analysed structures is replaced by the ensemble of the MD snapshots ). But I've heard that there is possible ways to extract normal modes indirectly from the output trajectories. James
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