Colvars in NAMD 2.7b4

From: Jérôme Hénin (
Date: Tue Sep 21 2010 - 07:06:29 CDT

Hi everyone,

As you may have noticed, NAMD 2.7b4 has just been released. This
version carries substantial improvements to the colvars module. We
encourage colvars users to switch to the new release.

Notable changes include:

1) all bugs reported on this mailing list have been fixed.

2) we have attempted to improve the documentation wherever unclear or
missing information has been brought to our attention.

3) the behavior of refPositionsFile and refPositionsCol has changed
slightly: refPositionsCol does not have a default value anymore. If it
is not specified, refPositionsFile expects a PDB file of the whole
system, coordinates are selected based on the atom numbers of atoms
making up the group. This is convenient when the group is defined
through atomNameResidueRange, as it removes the need for tagging the
relevant atoms explicitly in the PDB file. For consistency,
atomsFileCol does not have a default value anymore.

4) new component: selfCoordNum, a variant of coordNum that can be
useful for studying (or biasing) aggregation within a class of

5) new option for distance-related components: forceNoPBC. If this
parameter is set, the component is not PBC-aware, and the distance
between the coordinates as maintained internally is used. Solves
problems arising when the meaningful distance is not the minimum-image
one (shortest one across PBCs), e.g. between two parts of a large
protein in a relatively small periodic cell.

The colvars module is actively maintained. Please report all
unexpected or buggy behavior, and do not hesitate to bring up feature
requests or suggestions for improvement.

Jerome and Giacomo

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