Hi,
To clarify what Jason said, it is an implementation of NEB where the force
is decoupled between a user-denoted subsection (Part) of a system.
Although the entire system is replicated for each bead along the path, the
NEB springs are only applied to this subsection of the system.
This means you can use explicit solvent and only apply NEB to the atoms of
your solute if you so choose, or if you have a good idea of a specific
transition that is interesting, you can of course apply NEB to only this
part of the system. However, the part of the system that does NOT have NEB
springs applied does respond to the force field and is simulated, and we
assume that the sampling of this part of the system is influenced by the NEB
part.
-Christina
On Thu, Sep 29, 2011 at 12:35 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Sep 29, 2011 at 12:16 AM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
>
> > > I think the P here means "Partial". It's part of Christina's
> > > (relatively)
> > > new re-implementation of NEB in sander. Someone in Carlos's group can
> > > correct me if I'm wrong here. To my limited knowledge of NEB, I think
> > > it's
> > > just an approach that doesn't need to replicate the entire system, but
> > > merely subsections of the system (like, for instance, a disordered loop
> > > or
> > > something). I think that means it'll require fewer beads, and probably
> > > other benefits I'm unaware of.
> >
> > "A Partial Nudged Elastic Band Implementation for Use with Large or
> > Explicitly Solvated Large Systems", Bergonzo, C., Campbell, A.J.,
> > Walker, R.C., Simmerling, C.,Int. J. Quant. Chem., 2009, 109, 15,
> > 3781-3790.
> > ^^^^^^^^^^^^
> > |
> >
>
> Ha. Probably would've been funnier if I had posted that citation :)
>
>
> >
> > ;-)
> >
> > I'd just not heard it called the acronym PNEB before. Needddd sleeeppp...
> > :-S
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > ---------------------------------------------------------
> > | Assistant Research Professor |
> > | San Diego Supercomputer Center |
> > | Adjunct Assistant Professor |
> > | Dept. of Chemistry and Biochemistry |
> > | University of California San Diego |
> > | NVIDIA Fellow |
> > | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > ---------------------------------------------------------
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may
> not
> > be read every day, and should not be used for urgent or sensitive issues.
> >
> >
> >
> >
> >
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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--
Christina Bergonzo
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Doctoral Student, Simmerling Lab
Center for Structural Biology
CMM Bldg, Room G90
Stony Brook University
Stony Brook, NY 11794-5115
Tel. 631-632-1560
Web: http://comp.chem.sunysb.edu
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Received on Thu Sep 29 2011 - 05:30:03 PDT
