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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Received on Thu Aug 04 2022 - 13:34:29 PDT
