[gmx-users] Normal Mode Analysis

[Justin A. Lemkul]

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.

http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis

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.

-Justin

> 
> 
>     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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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