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 <jalem...@vt.edu> wrote: > > > James Starlight wrote: >> >> Mark, >> >> 2011/10/26 Mark Abraham <mark.abra...@anu.edu.au >> <mailto: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? >> > > 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
