?Dear Amber development team,
in the new implementation of the Amber 20 package we found a Random Acceleration module to simulate ligand egress from binding sites.
Locking at the code ramd.F90 it looks like the direction of the random force is chosen with random angles. However, this method will cause a bias of directions towards the poles of the chosen coordinate system. See a nice description of the problem here:
http://corysimon.github.io/articles/uniformdistn-on-sphere/?
This would cause an oversampling of some directions.
Best,
Stefan Richter
Molecular and Cellular Modeling Group (MCM)
HITS gGmbH
Schloss-Wolfsbrunnenweg 35
69118 Heidelberg
Germany
phone: +49 - 6221 - 533 279
fax: +49 6221 533298
email: Stefan.Richter.h-its.org
http://www.h-its.org
_________________________________________________
Amtsgericht Mannheim / HRB 337446
Managing Directors:
Dr. Gesa Schönberger
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 22 2020 - 08:30:03 PDT
