From: Jason Swails (jason.swails_at_gmail.com)
Date: Thu Jul 09 2015 - 20:05:36 CDT
On Thu, Jul 9, 2015 at 8:00 PM, Leonardo Herrera <ldhz04_at_remove_yahoo.com.mx
> Hi users
> I am searching a protocol to Running constant pH molecular dynamics
> 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 (
http://ambermd.org/tutorials/advanced/tutorial18/) and fairly complete
documentation in the Amber reference manual to help you get started.
-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher
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