Re: [AMBER] weird output of SMD simulation combined with Constant pH

From: Jason Swails <>
Date: Mon, 7 Dec 2015 15:14:30 -0500

On Mon, Dec 7, 2015 at 2:38 PM, Gustavo Seabra <>

> Are the ionizable residues part of the “pulling group” or “reference
> group” definitions? If so, is there a way to try some other definitions for
> the groups that do not include residues that may change in the course of
> the simulation?

​That shouldn't matter since the only thing that changes are charges. The
issue here is that the integrator is called to relax solvent distributions
in the middle of the regular MD. This is probably confusing the SMD code
(it thinks that the relaxation steps are "real" steps, which they are not).

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 07 2015 - 12:30:03 PST
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