How long are the implicit and explicit solvent simulations? Comparing both
simulations is pretty tricky. For instance, 1 ns implicit solvent
simulation can correspond to 5-10 ns explicit solvent simulation (you
might need to compare the rmsd vs. time graphs of implicit and explicit
solvent simulations for this matter).
On Mon, 27 Nov 2006, Marie-Pierre Durrieu wrote:
> Dear all,
>
> I have done a GB simulation (with the option igb=2) and a water
> simulation on a long helicoidal system. According to experiences my
> protein is very stable, so I expect the alpha helices not to deform too
> much during simulations.
>
> The trouble is the GB simulation loses almost 50% of the (n,n+4)
> hydrogen bonds present in the water simulation. Is it alarming ? Is GB
> known for destructuring alpha helices ? Or is GB only exploring more
> conformational space ?
>
>
> Thanks in advance,
>
>
> Marie-Pierre.
>
>
--
Ilyas Yildirim
---------------------------------------------------------------
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- http://www.pas.rochester.edu/~yildirim/ -
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Received on Wed Nov 29 2006 - 06:07:34 PST
