Re: How to do pH simulation on NAMD?

From: Jérôme Hénin (
Date: Fri Jul 16 2004 - 05:00:03 CDT

Xin Chen,

How is pH described in the framework of a molecular mechanics force field ?
By the protonation state of acidic/basic groups, which doesn't change
throughout a simulation.

This should answer your question.

PS : You can find discussions on related topics in the archives of this

Xin Chen wrote :

>Dear NAMD developers and users,
>I wonder if there is a method in NAMD that I can do constant pH simulation
>for protein? I want to study the properties of a protein at a certain pH
>value. Thank you very much.
>Sincerely yours,
>Xin Chen

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