This may sound stupid...but as far as i have read, most of the force field
parameterization and torsion angle correction involves extensive testing on
DNA/RNA duplexes. Testing on loops have been limited to tetraloops
(UUCG/GNRA) which are very short and less prone to structural fluctuations
(extensive base stacking and hydrogen bonding). If the loop length is long
( 7-8 nucleotides in my case) and all i am interested is in looking for
stability of hydrogen bonds between these loops and duplex RNA stems, then
how long is long enough? will 300-600ns give me a good estimate ? (provided
the fact that i don't have access to a GPU machine, this long simulation
will take ages to finish)
Thanks for the replies...
On Mon, Sep 1, 2014 at 9:20 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> not really. imagine that you instead carried out 600,000 simulations of 1ps
> each (still 600ns total). none will go far from the initial structure and
> you would not expect to see motions that occur in 600ns. the issue is
> somewhat complex, and depends a lot on whether you are looking at something
> that obeys first orders kinetics and so on. the folding.home people have
> done a lot of work in this area, since they tend to have many relatively
> short simulations. Also, even if it is first order kinetics, the rate
> constant will determine a probability of seeing an event in a certain
> timescale. our simulations do not normally have the number of independent
> events needed for them to show statistical behavior that might match up to
> an experiment on a particular timescale. so, as Dave Case mentioned, if the
> "events" that you see occur on a similar timescale to the length of the
> simulation, you an't say much specific about whether another simulation
> would or would not see the same behavior, or if it is significant that
> another simulation does not.
>
> In your specific case, you should probably look into what others have seen
> in their simulations of loops, since a fair number of studies have been
> published in that area. I agree with DAC, 200 or even 600ns is not very
> long. Much depends on the initial structure and what type of dynamics you
> are trying to study.
>
>
> On Mon, Sep 1, 2014 at 9:38 AM, Asmita Gupta <asmita4des.gmail.com> wrote:
>
> > But, then i have 3 different runs for the same system, each 200ns. Is it
> > incorrect to say that the system has experienced conformational sampling
> > for a total of 600ns, which might be long enough for loops?
> >
> > Asmita
> >
> >
> > On Mon, Sep 1, 2014 at 5:54 PM, David A Case <case.biomaps.rutgers.edu>
> > wrote:
> >
> > > On Mon, Sep 01, 2014, Asmita Gupta wrote:
> > > >
> > > > In 2 out of 3 trajectories, the structure is experiencing a loop
> > residue
> > > > backbone flipping (zeta, chi and delta), after which it remains
> stable.
> > > > However, with parmbsc0, this residue flipping is not observed at all,
> > > > neither with YIL chi correction.
> > >
> > > One useful analysis is to see how long it took for the flip to take
> place
> > > in
> > > the two trajectories where it did happen. If these are significant
> > > fractions
> > > of the 200 ns length, then it is plausibly just a matter of chance that
> > you
> > > did not see such behavior in the third run. You could extend the third
> > run
> > > longer to see what happens.
> > >
> > > >
> > > > is 200ns enough for a good conformational sampling?
> > >
> > > This is not sufficient in general to sample RNA loop configurations.
> > >
> > > ....dac
> > >
> > >
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Received on Mon Sep 01 2014 - 10:30:02 PDT
