Re: [AMBER] REMD hybrid solvent model

From: Hosein Geraili Daronkola <geraili.hsn.gmail.com>
Date: Wed, 11 Mar 2020 18:13:35 +0100

Carlos, why do you think it is not appropriate? What do you propose?
I just want enough sampling of the unfolded protein.

Best




On Wed, Mar 11, 2020 at 4:39 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:

> 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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-- 
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 - 10:30:02 PDT
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