Re: regarding constant PH simulation

From: Jeff Comer (
Date: Thu Nov 19 2020 - 21:25:24 CST

(1) I don’t think there is any explanation on how to do this. You have to
study the files included in the tutorial (and distributed with NAMD) as a

(2) This is issue is discussed in the paper
( ). If I recall correctly, the
answer is that it doesn’t matter. The idea that PME with charged systems
automatically leads to erroneous results is mostly a myth. Artifacts are
found for small and highly charged systems, but are negligible for most
modern systems with large enough water boxes.


On Thu, Nov 19, 2020 at 21:09 zahra nabavi <>

> Dear NAMD Community,
> I have two questions regarding constant PH simulation.
> 1- I am planning to use it for a new molecule but as far as I know it
> only works for aminoacids. What changes do I need to make so I could use it
> for protonation of my own molecule? Is there any tutorial or guide to help
> me make required changes to the TCL and input files?
> 2- When we change protonation states from protonated to deprotonated
> states or vice versa, are there any "ghost" hydrogens somewhere in the
> system to compensate for the movement of the charge between solvent and the
> aminoacid? and if not, isn't it going to affect the PME calculations?
> Thank you in advance,
> Zahra

Jeffrey Comer, PhD
Associate Professor
Department of Anatomy and Physiology
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

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