[gmx-users] ED sampling

[Bert de Groot]

Thomas Stockner wrote:
> Dear Gromacs users,
> 
> I am trying to use ED sampling, but some details remain unclear.
> How is the parameter "slope" (nm/step), specified with make_edi, exactly 
> calculated (defined)? Is it an average over the last X steps?

it's a running  average over the last 500 steps (usually ps).

> Are bond constraints (LINCS) applied after atoms (e.g. CA) are projected 
> along the eigenvectors in case of rejection of the MD step?
> 

edsam is called after lincs (or shake), as an additional coordinate constraint.
no MD step is "rejected" btw. edsam either accepts a step as is, or it corrects
the position along selected eigenvectors, if required.

Bert

________________________________________________
Bert de Groot, PhD

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de
http://www.mpibpc.mpg.de/groups/de_groot