Ok...all the simulations are 200ns long...and this fraying is observed
after 50ns and lasts till 100-150ns..but what is an "activated
event"....also, none of the fraying effects observed in ff12sb were there
when i used CHARMM36..so is it a force field dependent process?
On Fri, Aug 2, 2013 at 5:54 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, Aug 02, 2013, Asmita Gupta wrote:
> >
> > I have multiple RNA helices of 36 base-pairs that i am simulating using
> > ff12sb(chi OL3 corrections). These structures differ in the identity of
> > their central two base-pairs.
> >
> > My doubt is that in some sets, the terminal base-pair fraying effect is
> > very large, to the extent that the base-pair completely opens up and then
> > reforms, while in other cases this effect is not observed at all..i.e.
> the
> > pair remains quite stable.
>
> This sounds perfectly normal. You don't say how long your runs are, but
> all
> simulations will eventually see some amount of terminal base-pair
> distortions
> of the type you mention. Since this is an activated event, the times at
> which
> such events occur will vary from one simulation to the next.
>
> ...dac
>
>
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Received on Fri Aug 02 2013 - 06:00:04 PDT
