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

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Fri Jun 05 2009 - 10:53:48 CDT

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
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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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