Re: 2.7b metadynamics ::hBond component :: folding of a single helix in water

From: Ali Emileh (
Date: Mon Jun 22 2009 - 14:23:57 CDT

Hi Giacomo,

Thanks for all the comments and guidance.
I never saw a negative value of the colvars in the simulation, just the
boundaries in the
log file and it got me worried, but I think the core of the colvars module
is working
just fine and producing alpha values of the right sign.

I thought I can forget about the alpha component and use a combination of
dihedrals and
hBond/distances to fold the helix for now. I started with a simple config
like this :

colvarsTrajFrequency 1000

colvar {
    name hb
    outputAppliedForce on

    hBond {

    acceptor {
        atomNameResidueRange O 100-105
        psfSegID G
    donor {
        atomNameResidueRange N 106-110
        psfSegID G


metadynamics {
    colvars hb
    hillWeight 0.04
    dumpFreeEnergyFile yes

I know it lacks boundaries. I just wanted to get the thing to work in steps.
But the problem
is I can't get it to recognize the colvar components. It gives me the erro :

colvars: Error: in parsing "acceptor".
colvars: If this error message is unclear, try recompile with
FATAL ERROR: Error in the collective variables module: exiting.

now when I change the component from hBond to coordnum and the atom groups
group1 and group2 (I can't get it to accept any group name other than these,
that "Error: definition for atom group "group1" not found."), it goes
through the component
recognition and parsing (at least it seems to do so) and gets stuck in the
"colvars: Tried
to initialize a count grid on variable with undefined boundaries" error
message which can
be fixed by defining boundaries (I DOES go into the simulation). So all I
can conclude
here is that I'm missing something in the atom groups definition.

Any thoughts on this will be highly appreciated.

Thank you,

On Wed, Jun 10, 2009 at 9:57 AM, Giacomo Fiorin <>wrote:

> Hi Ali, I see: what you mean (narrowing a1 to an interval of interest) is a
> good idea, but to do so you also need to set some force constants at
> the two boundaries. Otherwise, those are just the limits of the grid, and
> they get expanded over time as the colvar moves outside of them. The
> fact that lowerBoundary goes negative can be worrisome, but it is only
> due to the
> fact that the code managing the grid doesn't know that a1 can't go
> negative, and allocates a buffer region.
> Of course, it's never 100% guaranteed that the code is free of bugs,
> especially at this stage. So, if you do observe negative values of
> the alpha variable in the .colvars.traj file, I'd like to know.
> You're applying small hills (0.04 kcal/mol) but very frequently (10
> steps), so you *are* pumping energy into it. Maybe the helix is just
> too stiff and by the time you've added energy to one structure
> metadynamics has moved it back to a similar one?
> This is why I suggest that you try the harmonic steering: you could,
> say, set a target of 1 to try and fold the helix completely. Unlike
> in metadynamics, at least you'd drive it monotonically there, and
> you'd have to cope with less complications.
> Otherwise, if your target is the folded helix, and the other
> structures are not relevant to you, it may simply be happening that
> because of the system's nature the colvar does not respond as quickly
> as you want it to, because other degrees of freedom need to be forced
> (i.e. additional colvars).
> Ciao
> Giacomo
> ---- ----
> Giacomo Fiorin
> Center for Molecular Modeling at
> University of Pennsylvania
> 231 S 34th Street, Philadelphia, PA 19104-6323
> phone: (+1)-215-573-4773
> fax: (+1)-215-573-6233
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> mail: giacomo.fiorin_<at>
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