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

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Tue Jun 09 2009 - 12:24:39 CDT

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/
---- ----

On Tue, Jun 9, 2009 at 6:52 PM, Ali Emileh<ali.emileh_at_gmail.com> wrote:
> Giacomo,
>
> Thank you for the reply.
> I removed the "conflicting" hillWidth line and now use these settings.
>
> width 0.04
>
> lowerBoundary 0.3
> upperBoundary 1.0
>
> hillWeight 0.04
>
> but it's behaving the same way. Of note, are two warning lines in the log
> file :
>
> colvars: Warning: colvar interval ( 3.00000000000000e-01 -
> 1.00000000000000e+00) is not commensurate to its width (
> 4.00000000000000e-02).
> ...
> ...
> ...
> colvars: Setting a new lower boundary for colvar "a1", at -0.38.
> colvars: Expanding the grids for the metadynamics bias "metadynamics1".
> colvars: Warning: colvar interval (-3.80000000000000e-01 -
> 1.00000000000000e+00) is not commensurate to its width (
> 4.00000000000000e-02).
>
> So it's ignoring my boundaries. I can't understand why.
>
> I have decreased the newhillfrequency parameter to 10, hoping that it will
> squeeze the
> protein into SOMETHING!, in hope of some CHANGE. Right now, metadynamics
> seems
> to have no visible effect. The forces output in the .traj file have
> increased to +/- 800-1000,
> and their absolute value seems to increase linearly with time. Does it mean
> its applying
> the forces? Do I need more time? By applying it to this small system, I just
> want to make
> sure that metadynamics works so I can move on and apply a similar
> configuration to my
> main system.
> Any thoughts about the above warnings and also what I should do to 'see'
> something?
>
> Thanks a lot,
> Ali
>
> On Fri, Jun 5, 2009 at 11:53 AM, Giacomo Fiorin <gfiorin_at_seas.upenn.edu>
> wrote:
>>
>> Hi Ali, the grid resolution is set by the "width" of a1: use that, and
>> only that, to change the resolution of the PMF.
>>
>> hillWidth, instead, is only a smoothing parameter because it is
>> multiplied to the number above as the documentation says, and should
>> never be set smaller than 1. If you set it to 0.02, all of the hills
>> become 0.02*0.04 = 0.0008 wide: way too narrow to have an effect.
>>
>> 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/
>> ---- ----
>>
>>
>>
>> On Wed, Jun 3, 2009 at 1:39 AM, Ali Emileh<ali.emileh_at_gmail.com> wrote:
>> > 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
>> > my
>> > 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.
>> >
>> > Ali
>> >
>
>

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