TMD comments

From: Michael Feig (
Date: Fri Jan 16 2009 - 23:06:07 CST

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
 Computer Science & Engineering
 Michigan State University, East Lansing, MI

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