From: Michael Feig (feig_at_msu.edu)
Date: Tue Jan 20 2009 - 21:27:31 CST
Thank you very much, Victor.
This is what I was looking for. The changes in GlobalMasterTMD.C
are in fact rather minor and with the fixes NAMD2.6 seems to work
for me.
I will look forward to using the 2.7 version when it is released.
It seems that there will be many new exciting features.
Michael.
---
Michael Feig
Biochemistry & Molecular Biology
Chemistry
Computer Science & Engineering
Michigan State University, East Lansing, MI
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
> Of V.Ovchinnikov
> Sent: Tuesday, January 20, 2009 10:39 AM
> To: Michael Feig
> Cc: namd-l_at_ks.uiuc.edu
> Subject: RE: namd-l: TMD comments
>
> Hi, Michael.
> You can see the changes made to the source here:
> http://www.ks.uiuc.edu/Research/namd/cvs2html/namd2_src.html
> The files you are interested in are GlobalMasterTMD.h and
> GlobalMasterTMD.C
>
> Victor
>
>
> On Tue, 2009-01-20 at 08:02 -0500, Michael Feig wrote:
> > Peter,
> >
> > do you (or anybody else) know if the bug fixes that would allow TMD to
> work
> > in parallel are minor and can be easily applied to the 2.6 version?
> >
> > If so, is it possible to post them to this list?
> >
> > I haven't heard back about getting CVS access but I am not sure I really
> > want to deal with a 2.7 version that might have other issues (being a
> pre-
> > release version). If I can get TMD working with 2.6 that would allow me
> > to go forward with the simulations I plan to run.
> >
> > Thanks,
> >
> > Michael.
> >
> > ---
> > Michael Feig
> > Biochemistry & Molecular Biology
> > Chemistry
> > Computer Science & Engineering
> > Michigan State University, East Lansing, MI
> >
> >
> > > -----Original Message-----
> > > From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
> Behalf
> > > Of Peter Freddolino
> > > Sent: Saturday, January 17, 2009 12:01 PM
> > > To: Michael Feig
> > > Cc: namd-l_at_ks.uiuc.edu
> > > Subject: Re: namd-l: TMD comments
> > >
> > > Dear Michael,
> > >
> > > 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.
> > >
> > > An even more elegant and general solution is present in the colvars
> > > module of namd (currently available in cvs, to be included with namd
> > > 2.7) contributed by Jerome Henin and Giacomo Fiorin. It allows the
> > > definition of several types of biasing potentials and their use with
> > > several biased dynamics methods. You should be able to find
> > > documentation in the ug subdirectory of the cvs tree.
> > >
> > > To answer your later question, the .tar.gz available through the
> webpage
> > > is *not* the cvs version; you need to instead follow the steps under
> the
> > > "Bleeding edge" heading at
> > > http://www.ks.uiuc.edu/Research/namd/development.html
> > >
> > > >
> > > > 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?
> > >
> > > You're correct as far as I can tell; this will have to be fixed in the
> > > documentation. Thanks for pointing it out.
> > >
> > > >
> > > > 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?
> > >
> > > You'll need to get the cvs version through the mechanism mentioned
> > > above. In any of the namd2.6 releases TMD will not work properly in
> > > parallel.
> > >
> > > >
> > > > 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.
> > >
> > > Please note that namd2.6 is at this point a bit over 2 years old,
> which
> > > is likely responsible for at least some of the difficulties you
> > > experienced. The binary releases are still fine, but if you're
> building
> > > from source I highly recommend using the development version. Please
> > > give the cvs version a shot (it also has updated release notes) and by
> > > all means let us know if you run into similar trouble so that things
> can
> > > be fixed before the 2.7 release.
> > >
> > > Best regards from an East Lansing native,
> > > Peter
> > >
> > > >
> > > > Thanks for any feedback.
> > > >
> > > > ---
> > > > Michael Feig
> > > > Biochemistry & Molecular Biology
> > > > Chemistry
> > > > Computer Science & Engineering
> > > > Michigan State University, East Lansing, MI
> > > >
> > > >
> >
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