[gmx-users] pca-based MD

Thomas Evangelidis tevang3 at gmail.com
Mon Sep 24 00:48:53 CEST 2012


thanks again for explanation. Its also intresting to me is it possible
> to do further biassed MD guided on that FMA modes as well as obtain
> projections onto that FMA sub-spaces of X-ray datasets for instance ?
> ( e.g for comparison of the results from FMA of experimental data as
> well as MD_data)
 Have a look at another thread posted today, named "PC comparison between
two simulations".

On a second thought, you might want to consider the nudged elastic band
method and its variants for your case, since you have the initial, the
final and intermediate states of your protein. Unfortunately they are not
implemented in GROMACS, but they are in AMBER.




Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/

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