Wow! I am amazed to see all of the great feedback just overnight. Christina
is absolutely correct about what I was referring to when I used PNEB. I am
not sure if I made up that extended acronym or if I had seen it somewhere.
Nonetheless, this was very helpful.
I will look into applying for free time through the NSF XSEDE. In the
meantime, however, I would be interested in any suggestions for alternative
approaches to simulating optimum energy paths between different
conformational states of an RNA. Much of what I know and am learning is
self-taught and I am currently the only person in my group that does
computational work, so I would be open to any and all suggestions. To expand
upon my problem, due to the highly polar nature of RNA, it is imperative
that any approach that I use has the ability to efficiently make use of
explicit solvent and positive ions (Na+ is best).
Dr Walker, thank you for your suggestion of using accelerated MD. I will
take the time to learn more about this method and most likely use this
mailing list as a lifeline if I have additional questions.
Thanks again!
Adieu,
Will
On Thu, Sep 29, 2011 at 8:25 AM, Christina Bergonzo <cbergonzo.gmail.com>wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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 - 06:30:02 PDT
