Re: TMD comments

From: Jerome Henin (
Date: Sat Jan 17 2009 - 19:52:40 CST

Hi Michael,
If you end up using the development version from CVS, you will have
access to the "collective variables" module, which provides various
ways to apply restraints on (among other things) RMSDs.

On Sat, Jan 17, 2009 at 12:06 AM, Michael Feig <> wrote:
> In learning about targeted MD (TMD) in NAMD I have
> encountered a few issues that I would like to share
> with the NAMD community.
> 1) I am interested in running TMD as a harmonic biasing
> potential with a fixed reference RMSD for a certain time
> (so that I can use appropriate equilibrium reweighting
> techniques). This doesn't work with the current version
> because the biasing term is only effective on one side
> of the final RMSD target value. This may be a feature
> for other purposes but in my case it makes TMD unusable.
> This can be easily fixed by replacing
> if ((finalRMS < initialRMS && targetRMS <= curRMS) ||
> (finalRMS >= initialRMS && targetRMS > curRMS)) {
> in lines 173-174 of GlobalMasterTMD.C with
> if (1) {
> A more elegant version could introduce an additional
> keyword that allows a selection of a one-sided or two-sided
> biasing potential.
> 2) The manual says that the biasing potential is
> U = k/2N [ RMS(t) - RMS*(t) ]^2
> After looking at the code and checking the derivatives I
> think that this is incorrect. I think the potential is in
> fact (as it should be):
> U = k/2 [ RMS(t) - RMS*(t) ]^2
> The 1/N factor comes in when calculating the derivatives/
> forces, but the force constant in the potential does *not*
> seem to be scaled by N in the current TMD implementation. Can
> the developers confirm that?
> 3) I have seen comments about problems with TMD in
> parallel runs and that those problems have been fixed in the
> 'CVS version'. Does that also apply to the source version
> (tar.gz file) that is available through the standard NAMD
> download mechanism or is the 'CVS version' a different version?
> 4) Finally, I have more general comments about the compilation
> instructions (in notes.txt) and default Makefiles that ship
> with the source distribution. They are not exactly up to
> date and result in a number of minor problems on standard
> modern UNIX distributions (in my case an EM64T system). In
> particular, recent versions of gcc don't seem to work, current
> versions of icc need different flags for generating static
> executables that won't crash upon startup, the charm test
> program is not where 'notes.txt' says it is etc. The problems
> all seem to be known more or less and can be solved with
> a little bit of help from Google but it would be nice if
> NAMD could be compiled out of the box on Linux
> workstations with recent compiler and OS versions.
> Thanks for any feedback.
> ---
> Michael Feig
> Biochemistry & Molecular Biology
> Chemistry
> Computer Science & Engineering
> Michigan State University, East Lansing, MI

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