mistakes in the user guide in the accelerated MD section ?

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Tue Jan 15 2019 - 07:29:02 CST

Dear NAMD users and developers,

I just noticed some potential mistakes in the NAMD user guide in the
section "accelerated MD".
In the description of the "accelMDdual", "accelMDTE" and "accelMDTalpha"
parameters, it is written that the second boost is applied on the
"Total-Dihedral" potential. However, in the dual boost flavor of aMD, as
described by Hamelberg et al (J.Chem.Phys. 2007) one boost is applied on
the DIHEDRAL energy and one on the total potential energy (and not on
the Total - Dihedral) .... Right ?

Assuming that the code applies the boosts correctly, it would be great
if the user guide is also corrected because it may induce confusion
especially for people new to the method.

Best wishes

Vlad Cojocaru, PD (Habil.), Ph.D.
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de

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