Thank you all for your help! As this will be a completely different topic, I
will create another thread to ask advice for choosing the best alternative
methods.
-Will
On Thu, Sep 29, 2011 at 9:13 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hi Will,
>
> On Thu, Sep 29, 2011 at 9:03 AM, William Cantara <wcantara.gmail.com>
> wrote:
>
> > 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).
> >
>
> Agreed. Although keep in mind that time scales in explicit solvent are
> much
> larger than in implicit solvent (due to real solvent viscosity). One thing
> to be careful about is that you should restrain your RNA system for a long
> time while you equilibrate solvent and ion positions around your system (it
> doesn't take much to destroy RNA structure in a simulation, from what I've
> been told).
>
> Also, when Ross was talking about accelerated MD, he was referring to a
> technique that was being implemented in pmemd currently and will
> (hopefully)
> be available for the Amber 12 release. (I just wanted to make sure you
> didn't miss that part). Thus, for the present time you should look into
> such methods as steered molecular dynamics (SMD) and umbrella sampling.
> Both of these are accessible through the CPU version of pmemd and are
> described in the manual.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Mon Oct 03 2011 - 18:00:02 PDT
