Re: [AMBER] REMD hybrid solvent model

From: Hosein Geraili Daronkola <geraili.hsn.gmail.com>
Date: Wed, 11 Mar 2020 16:35:21 +0100

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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


-- 
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
Received on Wed Mar 11 2020 - 09:00:02 PDT
Custom Search