2.7b metadynamics ::alpha module :: folding of a single helix in water

From: Ali Emileh (ali.emileh_at_gmail.com)
Date: Tue Jun 02 2009 - 18:39:25 CDT

Hi all,

I have been trying to use metadynamics to fold a simple alpha helix (16
residues long)
without any success. Contacting the module authors, I refined my Gaussian
sizes (which
were too broad) but still can't get it to work and the alpha colvars I have
defined doesn't
look to be changing much other than what you would expect from a normal MD.
During a
10 ns run, it barely changed from the strating value of ~0.44 to ~0.5 toward
the end. I had
set a lowerboundary of 0.5 for the colvars but I'm guessing since it started
lower than that,
it might be ignoring the boundary? In the starting conformation, the helix
is half folded and
I have used TMD before to easily fold it in the context of its parent
molecule (this is an
excised helix I'm using to learn about the metadynamics module). This is how
COLVARS.CONF file looks like:
colvarsTrajFrequency 1000

colvar {
    name a1
    width 0.04
    outputAppliedForce on
    lowerBoundary 0.4
    upperBoundary 1.0

    alpha {
        residueRange 100-116
        psfSegID G

metadynamics {
    colvars a1
    hillWeight 0.05
    hillWidth 0.02
    dumpFreeEnergyFile yes

I have tried lower boundaries of 0.3 and 0.5 and also hillweights and widths
of (0.4,0.2,0.1) (0.02,0.05,0.1),
respectively. None worked.

I would highly appreciate ant input.

Thank you.


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