AMBER Archive (2006)

Subject: Re: AMBER: helices in GB simulations

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Nov 27 2006 - 16:09:04 CST

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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