Re: Running constant pH molecular dynamics (CpHMD)

From: Jason Swails (
Date: Thu Jul 09 2015 - 20:05:36 CDT

On Thu, Jul 9, 2015 at 8:00 PM, Leonardo Herrera <
> wrote:

> Hi users
> I am searching a protocol to Running constant pH molecular dynamics
> (CpHMD).
> Anybody can help me?

​I don't think that NAMD implements a CpHMD protocol. The only papers that
I've seen that use CpHMD use either Amber, CHARMM, or GROMACS. I think the
most refined models are implemented in Amber and CHARMM.

If you don't have a paid license for CHARMM, then your best bet is probably
the free "sander" program from AmberTools that implements a couple CpHMD
algorithms. There is even a tutorial ( and fairly complete
documentation in the Amber reference manual to help you get started.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher

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