[gmx-users] Normal Mode Analysis
tsjerkw at gmail.com
Wed Oct 26 15:41:25 CEST 2011
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 :)
On Wed, Oct 26, 2011 at 2:57 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> James Starlight wrote:
>> 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
> 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.
> 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
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Tsjerk A. Wassenaar, Ph.D.
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
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