can TMD alignment prior to force calculation be turned off?

From: Michael Zimmermann (
Date: Sun Jan 08 2012 - 15:04:15 CST

Dear NAMD community,

I have been reading the 2.8 user's guide for SMD, TMD, harmonic restraints,
rmsd colvars, etc. as well as the mailing list archive for the best
solution to the general problem of "I would like pull a structure to a
reference conformation" subject to the following:
1) only a subset of the atoms need to significantly move in space
2) they need to achieve a precise final conformation (so not SMD)
3) the atoms that don't need to be directed can't be fixed in space -
ideally they would be simply unconstrained (so, not TMD)

I say not TMD because if I (1) only tag some atoms as TMD atoms, they will
be aligned before the forces are calculated (thus no "pulling" through
space will occur), or (2) tag all (or a sufficiently large subset) atoms as
TMD, but now there are constraints added to the atoms that I would like to
be unconstrained. The rmsd colvar routine also aligns prior to force

The most convenient solution would be a parameter that allows me to turn
the alignment off in TMD or rmsd colvars. I have been unable to find such
an option.

To some extent, *TMDDiffRMSD *could accomplish this, but I don't want the
structure to back-track to the first conformation.

I am presently using a custom tclforces script to add forces specifically
where I want them, but this code is difficult and time consuming (for me)
to maintain. If there is a way to turn off the alignment in TMD (that is,
prevent the TMD atoms from being spatially superimposed prior to force
calculation), would you be so kind as to help me with the syntax? I have
been unable to find something like it in the archive or User's Guide.

Thank you,

Michael T. Zimmermann

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