On Wed, Oct 06, 2010, Ali M. Naserian-Nik wrote:
>
> I am a PhD student of applied mechanics. I am going to simulate double
> stranded DNA pulling in implicit environment, using generalized Born
> solvent model. But I do not know that if igb=2 and igb=5 can be used
> for this purpose, as they have been used for proteins. I tested the
> three option, i.e., igb=1, igb=2, and igb=5 and found some structural
> differences during stretching of DNA, especially between the case
> igb=5 and the two other cases.
As the manual states (p. 56) almost all published work on nucleic acids has
used igb=1; we have anecdotally seen bad behavior with other values, but have
not pursued this very far. If you want to try other values, you should
carefully assess their results for ordinary simulations before going on to
pulling experiments.
....dac
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Received on Wed Oct 06 2010 - 05:00:04 PDT
