Re: [AMBER] Implicit solvent simulation effects for the folding

From: Hai Nguyen <>
Date: Mon, 5 Nov 2018 23:16:50 -0500

Which GB model + force field you're using?
Just make sure your simulation is converged (e.g: starting from two initial
structures and getting similar popular between 2 simulations).

In general, it's hard to do the right thing random coil structure since
lots of GB models tend to favor more compacted topology.


On Mon, Nov 5, 2018 at 10:18 PM Mijiddorj B <> wrote:

> Dear Amber Users,
> I would like to discuss about the effects of implicit solvents for the
> folding simulation. I used the implicit Generalised Born solvent for the
> linear structure of amphipilic peptides based on the sequence. I simulated
> 100 ns, and I was formed alpha helical structure. Experimentally, it shows
> random coil structure in the water.
> What do you think? please advice me.
> Best regards,
> Mijiddorj
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Received on Mon Nov 05 2018 - 20:30:02 PST
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