Re: can TMD alignment prior to force calculation be turned off?

From: Michael Zimmermann (
Date: Sun Jan 08 2012 - 17:03:41 CST

Thank you for the reply Axel.

You are correct in evaluating that ambiguity - I do generally mean
positional restraints (tho there is an accompanying change in
conformation). My missinterpretation of the description of the
*consref *parameter is to blame for not catching that it could be used
in this way (I
read it as the initial position would be taken from the reference file, not
the "reference position"). I just ran a test simulation and it looks like
this type of constraint will work.

Thank you for your time.

On Sun, Jan 8, 2012 at 3:19 PM, Axel Kohlmeyer <> wrote:

> michael,
> On Sun, Jan 8, 2012 at 4:04 PM, Michael Zimmermann <>
> wrote:
> > 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
> > calculation.
> please clarify one detail. i don't quite understand
> why it matters so much to you to not align the reference
> to the current state, if you care about conformation.
> conformation in my understanding are the relative
> coordinates of a group of atoms. if you turn off this
> alignment, you have what i would call "position restraints"
> and thus your goal would be to direct atoms to specific
> positions, and not only to a particular conformation.
> so if i am right, then you should just do the opposite
> of what people do to carefully equilibrate a system,
> i.e. define position restrains and gradually increase
> (not decrease) the force constant.
> if you don't need to reach specific coordinates in space,
> then you should explain where the difference lies.
> thanks,
> axel.
> >
> > 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
> --
> Dr. Axel Kohlmeyer
> College of Science and Technology
> Temple University, Philadelphia PA, USA.

Michael T. Zimmermann
Ph.D. in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University

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