Dear Hai,
Thank you very much for your prompt reply. I used the "standard" pairwise
generalized Born model using the default radii with amber.ff14SB.
Best regards,
Mijiddorj
On Tue, Nov 6, 2018 at 1:17 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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.
>
> Hai
>
> On Mon, Nov 5, 2018 at 10:18 PM Mijiddorj B <b.mijiddorj.gmail.com> 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 - 21:00:02 PST
