Just to add to what Koushik said, an unfolded protein of that length will
require a massive box of water to enclose unfolded states. The hybrid
solvent model in Amber is only used during the exchange step ; md is still
carried out in this large box. It also sounds like you intend to
extensively sample conformational space during this run. I think working on
the project you describe will take very significant computational
resources. You may want to look at work from DESRES using Anton.
On Tue, Mar 10, 2020, 4:25 PM koushik kasavajhala <koushik.sbiiit.gmail.com>
wrote:
> Hi Hosein,
>
> Do you want to do a MD simulation with hybrid solvent or do you want to do
> Replica Exchange MD simulation with a hybrid solvent Exchange scheme?
>
> The point you mentioned pertains to Replica Exchange MD (REMD) using a
> hybrid solvent exchange scheme. Hybrid solvent REMD using pmemd (to be
> released with AMBER 20 version) allows systems with Na+, Cl-, and K+ ions
> only. To my knowledge, hybrid Solvent REMD in sander does not support
> systems with ions.
>
> For a big system like yours, it may not be ideal to do explicit solvent
> REMD. Is there a reason why you do not want to use GB with saltcon set to
> some value?
>
> Best,
>
> Koushik
>
> On Tue, Mar 10, 2020 at 4:09 PM Hosein Geraili Daronkola <
> geraili.hsn.gmail.com> wrote:
>
> > Hi all,
> >
> > I want to sample better my unfolded 129 residue protein in a high
> > concentration of salt. The system is quite big, with 40000 water
> molecules.
> > I want to use the hybrid solvent model for it, but what does this
> > sentence mean?
> >
> > * 2. Explicit counterions should probably not be used.*
> >
> > in the *caution *section of the *Replica exchange using a hybrid solvent
> > model *part of the 2018 manual.
> >
> > Best
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> >
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Received on Tue Mar 10 2020 - 19:30:02 PDT
