Solvent properties do not change.
On Mon, Jul 18, 2022, 1:21 AM Dulal Mondal via AMBER <amber.ambermd.org>
wrote:
> Hi,
>
> My question is do the solvent properties remain unchanged in the course of
> pH change? How are these properties controlled during CpHMD in explicit
> solvent?
>
> With regard,
> Dulal Mondal
>
> On Sat, Jul 16, 2022 at 1:14 PM Vinicius Wilian Cruzeiro <
> vwcruz.stanford.edu> wrote:
>
> > Hello Dulal,
> >
> > Although the MD is done in explicit solvent, for the Monte Carlo steps
> > where protonation state changes are attempted it is used implicit
> > solvent. The free energies for the reference compounds (that are stored
> in
> > the library used by cpinutils.py to construct your CPIN file) have been
> > computed with a salt concentration of 0.1 M and igb=2, so you should not
> > change these values unless you recompute the reference free energies
> > yourself.
> >
> > Please let me know if you have any further questions,
> > I hope this helps,
> >
> > *VinÃcius Wilian D. Cruzeiro, PhD*
> > Postdoctoral Researcher
> > Department of Chemistry
> > Stanford University
> > Twitter: .vwcruzeiro
> > ------------------------------
> > *From:* Dulal Mondal via AMBER <amber.ambermd.org>
> > *Sent:* Saturday, July 16, 2022 12:31 AM
> > *To:* amber.ambermd.org <amber.ambermd.org>
> > *Subject:* [AMBER] Constant pH Molecular Dynamics Simulation
> >
> > Dear Sir/Madam,
> >
> > I am running CpHMD Simulation at different pH in explicit solvent. I am
> > simulating the system at pH ranging between 3.0 and 10.0 with the
> increment
> > of 1.0 pH unit. I have a simple question regarding the explicit solvent
> > properties ( like dielectric constant, ionic strength etc.). How are
> these
> > properties maintained during pKa calculations?
> >
> >
> > With regards,
> > Dulal Mondal
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Aug 04 2022 - 13:34:30 PDT
