Re: regarding constant PH simulation

From: zahra nabavi (
Date: Fri Nov 20 2020 - 11:15:36 CST

Thank you very much Brian for clarifying this for me. So I am going to read
the cph36 more carefully.

On Fri, Nov 20, 2020 at 7:31 AM Brian Radak <> wrote:

> 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 We experimented with some other unpublished parameters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.
> Cheers,
> Brian
> 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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