Re: [AMBER] REMD hybrid solvent model

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Wed, 11 Mar 2020 13:32:33 -0400

well the hybrid solvent REMD method is a REMD variant that uses the hybrid
solvent only in the exchange, in order to reduce the number of replicas
that are needed. I'm not aware of and REMD simulation on an unfolded
protein in explicit water than has been reported to work... and the hybrid
method reduces the number of replicas, but also uses implicit
solvent during the exchange and explicit salt that you desire has never
been tested to my knowledge. You might be able to adapt it, but you would
need to determine how to treat the explicit ions in the implicit water,
which can be a real challenge. You would need to change the code as well.
You might want to look into similar methods such as REST and see if they
might be appropriate.
I don't mean to dissuade you from the study, just to point out that your
planned use has not been tested, and there are good reasons to think it
will not work without some significant changes.
carlos

On Wed, Mar 11, 2020 at 1:14 PM Hosein Geraili Daronkola <
geraili.hsn.gmail.com> wrote:

> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Mar 11 2020 - 10:30:03 PDT
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