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

From: Ali Emileh (ali.emileh_at_gmail.com)
Date: Tue Jun 09 2009 - 18:02:12 CDT

Hi,

About the warning messages :
My concern is that it seems the amount of time/force I'm giving the system
to 'diffuse' along
the colvar is not enough. So I was thinking by limiting it to build up the
Gaussians in a
restricted region, I'll get the system to change (saturate the energy wells)
in a shorter
amount of time. Please correct me if I'm wrong.

This is the complete config file :
===================================
colvarsTrajFrequency 1000

colvar {
    name a1
    width 0.05
    outputVelocity on
    outputAppliedForce on
    lowerBoundary 0.3
    upperBoundary 1.0

    alpha {
        residueRange 100-116
        psfSegID G
    }
}

metadynamics {
    colvars a1
    hillWeight 0.04
    dumpFreeEnergyFile yes
    newHillFrequency 10
}
===================================
This config is used in a run I have going now. The .traj file doesn't show
much
difference after about 0.5 ns.

The peptide is almost half-folded (as the starting value of the colvar
shows; ~0.4)
and my guess is the alpha colvar varies 0.0-1.0. Now I don't get the
negative value
for the colvar, especially for a partially folded helix. The dox say this
component
returns positive values. Is it possible there's a small error in how the
formula is
implemented?

I'm not using the extendedLagrangian option and the documentation says it
should
be off by default. So I'm assuming thats the case.

About the harmonic restraint, I'll give it a try as soon as I sit down and
read about
what it does. Thank you for the helpful work around.

Thank you,
Ali

On Tue, Jun 9, 2009 at 1:24 PM, Giacomo Fiorin <gfiorin_at_seas.upenn.edu>wrote:

> Hi Ali, the messages you've found are generated by two minor flaws in
> the code, which do not affect the dynamics. The Warning about the
> commensurate boundaries arises improperly, due to how we test that
> condition in the code, and will be fixed in the next release.
> Instead, why the boundaries change is because the code tries to
> accommodate all values that are explored within the run, according to
> expandGrids. By default this flag is on, which is inconsistent with
> what I wrote in the documentation: again, this is not your fault. But
> this flag only changes the length of the PMF anyway (and not its
> resolution), and most of all does not affect the trajectory that
> seriously.
>
> Can you send the complete configuration?
>
> One thing your msg says is that you are indeed exploring low values
> (little higher than -0.38) of the a1 colvar, well below the 0.3
> boundary you initially set: the peptide structure should be mostly
> unfolded near zero.
>
> Are you maybe using the fictitious particle of the extended
> Lagrangian? In that case, what you see moving would not be the
> physical value, but that of the fictitious particle, absorbing all the
> energy but not transmitting it to the atoms as it should. The
> optional extendedLagrangian flag can be useful in some cases, but it's
> not required to obtain a PMF, and it's often a good idea to ignore it,
> because things like this could occur if the force constant and mass
> hit one of the resonance frequencies of the system.
>
> If you just want to test the variable, I suggest a simpler approach:
> skip metadynamics, and do a steering through the harmonic restraint,
> setting the initial restraint center at the initial value and a target
> center away from it. You can then control in how many steps to move
> it there. If you see the trajectory following a straight line with
> some oscillations, then the colvar works for your system.
>
> Bests
> 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
> mobile: (+1)-267-324-7676
> mail: giacomo.fiorin_<at>_gmail.com
> web: http://www.cmm.upenn.edu/
> ---- ----
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:51:04 CST