Re: regarding constant PH simulation

From: Brian Radak (
Date: Fri Nov 20 2020 - 07:31:12 CST

Hi Zahra,

You are correct on item 1, we only parameterized CHARMM36 amino acids in
a published work. We experimented with some other unpublished parameters
(e.g. acetic acid), but those are not in the toppar tree. At one point I
was circulating a draft developer's guide, but I'm not sure this ever
made it onto the TCBG website. If you contact me offline I can forward
you a copy. I also took great pains to heavily comment the cph36 toppar
files, so I would encourage you to read those.

For item 2, the answer is actually very much that "it depends." For
purely aqueous or ionic solvated systems with reasonably large boxes, we
could not detect any significant PME artifacts. However, the artifacts
can be /substantial/ when modeling membrane systems. We discussed a post
hoc correction in the paper, but it is a bit cumbersome as it requires
shifting the pH range. I'm not sure if anyone is actively working on the
compensating charge solution and development never left the planning stage.



On 11/19/20 10:25 PM, Jeff Comer wrote:
> (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 guide.
> (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.
> Jeff
> On Thu, Nov 19, 2020 at 21:09 zahra nabavi <
> <>> wrote:
> 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
> Website:

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