bugfixes in the colvars module (ABF, metadynamics etc.)

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Wed Jun 24 2009 - 16:00:27 CDT

Dear users of the collective variables module (NAMD version 2.7b1):

Three bugs have been identified and fixed in the new NAMD source files
that you can download from the CVS repository. Note: the changed
colvar* files may also be downloaded individually from the CVS tree
and recompiled together with the now older NAMD 2.7b1 source tree.

- Incorrect Jacobian term in the system forces (used in ABF) acting on
the RMSD variable (symptom: slight systematic errors in the PMFs).
See Jerome Henin's message "Bug advisory: RMSD and ABF". The correct
formula has now been implemented.

- Mis-wrapping of the coordinates read from refPositions or
refPositionsFile (symptom: for certain systems, read distorted
reference coordinates and compute an incorrect roto-translation).
Note: this bug did NOT affect the refPositions or refPositionsFile
keywords of the "rmsd" and "orientation" variables, only those used
internally to the atom groups (i.e. those used in conjunction with
"centerReference" and "rotateReference"). If, starting from the very
first time step, you noticed unphysical values for the colvars that
made use of centerReference or rotateReference, this bug may have been
the origin. This bug did NOT affect simulations that never used
centerReference or rotateReference.

- Defining atoms from the columns of PDB files (atomsFile, atomsCol,
atomsColValue): the bug prevented to define atoms from PDB files,
leaving only the other options available (atomNumbers,
atomNameResidueRange). Now the (often more convenient) PDB file-based
atom definition is available.

Thank you and apologies for any inconvenience.

This code is still beta: please report any error message inconsistent
with the input syntax, or unphysical result that arises in the very
first steps of a colvars-based calculation.


---- ----
 Giacomo Fiorin
   Center for Molecular Modeling at
     University of Pennsylvania
     231 S 34th Street, Philadelphia, PA 19104-6323
 phone: (+1)-215-573-4773
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 mail: giacomo.fiorin_<at>_gmail.com
 web: http://www.cmm.upenn.edu/
---- ----

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