[gmx-users] Normal Mode Analysis

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 26 14:57:59 CEST 2011

James Starlight wrote:
> Mark,
> 2011/10/26 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at 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?

You should probably be using it.


Note that increasing emtol from 100 to 1000 actually makes your results worse, 
since mdrun will stop when the maximum force is below 1000 kJ/mol-nm, which is 
orders of magnitude too high for NMA.


>     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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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