Re: [AMBER] REMD hybrid solvent model

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Wed, 11 Mar 2020 11:39:32 -0400

Unfortunately this method is not really appropriate for your needs, in my
opinion.

On Wed, Mar 11, 2020, 11:36 AM Hosein Geraili Daronkola <
geraili.hsn.gmail.com> wrote:

> Hi Koushik,
>
> Yes, I mean Replica Exchange MD simulation with a hybrid solvent Exchange
> scheme.
>
> The reason for using the explicit solvent is because I want to compare it
> with the native structure in the explicit solvent, and also the salt
> concentration is very high (2 mol/kg).
>
> Thanks for the help
>
>
>
>
>
> On Tue, Mar 10, 2020 at 9:24 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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>
>
> --
> Hosein Geraili Daronkola
> Ph.D. student,
>
> Wissenschaftspark Potsdam-Golm
> Max Planck Institute of Colloids and Interfaces
> Theory and Bio-Systems Department
>
> Office K-1.119
> Am M├╝hlenberg 1 OT Golm
> 14476 Potsdam
> Germany
>
> Phone: +49-(0)331 567-9611
> Fax: +49-(0)331 567-9602
> E-mail: hosein.geraili.mpikg.mpg.de
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Received on Wed Mar 11 2020 - 09:00:03 PDT
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