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 Thu Sep 29 2011 - 06:30:04 PDT
