[gmx-users] ED sampling
Bert de Groot
bgroot at gwdg.de
Thu May 12 18:27:22 CEST 2005
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 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
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