[gmx-users] Normal Mode Analysis

[Tsjerk Wassenaar]

Hi James,

Regarding PCA and NMA congruency, they are different things, unless
the energy landscape consists of a single harmonic potential well. The
principal components and the normal modes will usually correlate quite
well, but if the simulation is sampling different energy minima, there
may be quite a difference. You can easily work that out graphically
for a two dimensional energy landscape :)

Cheers,

Tsjerk

On Wed, Oct 26, 2011 at 2:57 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>
>
> --
> ========================================
>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands