Re: [AMBER] Constant pH Molecular Dynamics Simulation

From: Vinicius Wilian Cruzeiro via AMBER <>
Date: Sat, 16 Jul 2022 07:44:39 +0000

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 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,

Vinícius Wilian D. Cruzeiro, PhD
Postdoctoral Researcher
Department of Chemistry
Stanford University
Twitter: .vwcruzeiro
From: Dulal Mondal via AMBER <>
Sent: Saturday, July 16, 2022 12:31 AM
To: <>
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
AMBER mailing list
AMBER mailing list
Received on Thu Aug 04 2022 - 13:34:26 PDT
Custom Search