Re: metadynamics combined with PCV

From: Anurag Sethi (anurag.sethi_at_gmail.com)
Date: Fri Jun 03 2011 - 14:11:54 CDT

Thanks Giacomo. I will probably send you a private email to figure out how
hard it is going to be to code the PCV approach.

Anurag

On Fri, Jun 3, 2011 at 11:28, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:

> Hello Anurag, the path collective variables (PCV) may be implemented
> in the near future, but at present it isn't. I'm currently working on
> other things.
>
> My guess is that unless you approximate the exponential functions with
> polynomials (which are implemented) you won't be able to define PCVs.
> And you can't use Tcl syntax to define a function of the existing
> collective variables. If you're extremely interested in using it and
> are fluent in C++ , we can communicate in private on how to start with
> either approach (native PCVs or Tcl-based).
>
> You may also want to have a look at PLUMED: it is not part of native
> NAMD and you wouldn't have certain features that you otherwise get
> with colvars, but it is more in sync with the variety of more recent
> metadynamics-based methods that are being developed by the Parrinello
> group.
>
> Giacomo
>
>
>
> On Fri, Jun 3, 2011 at 7:14 PM, Anurag Sethi <anurag.sethi_at_gmail.com>
> wrote:
> > Hi,
> >
> > I am trying to run metadynamics with NAMD 2.8b1 to study conformational
> > changes associated with allostery in HIV envelope proteins. I would like
> to
> > use the approach suggested by the Parrinello group in which they combine
> > path-based methods with the approach of collective variables and apply
> > metadynamics to study coformational changes in small peptides
> (Branduardi,
> > et al., J. Chem. Phys., 126:054103 (2007)) and kinases (Berteotti, et
> al.,
> > J. Am. Chem. Soc., 131:244-150 (2009)). In this method, they identify a
> > putative path by generating a morphed path from the initial conformation
> (A)
> > to the final conformation (B). After this, they define two path
> collective
> > variables (PCVs). One of these PCVs (s in their notation) measures the
> > "progress" along the putative path while the other PCV (z in their
> notation)
> > measures the "distance" of the conformation from the putative path.
> Using
> > this method, they are able to find multiple pathways for conformational
> > changes using metadynamics (in combination with the nudged elastic band
> in
> > their case).
> >
> > Both these PCVs use exponential functions of RMSD of the protein from
> > multiple conformations (defined by the putative path) of the protein. It
> is
> > equations 1 and 2 in the 2007 paper referenced above. I have read the
> > documentation for the colvars module in NAMD and see that RMSD is one of
> the
> > colvars defined in NAMD. However, I also see that polynomial functions
> of
> > these colvars can be used in NAMD directly. Is there any way for me to
> use
> > tcl along with NAMD to define these PCVs and run metadynamics on these
> PCVs?
> >
> > Thanks for your help,
> > Anurag
> >
>

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