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 - 05:30:02 PDT
