You can look at the details in
Enhancing Conformation and Protonation State Sampling of Hen Egg White
Lysozyme Using pH Replica Exchange Molecular Dynamics
Jason M. Swails and Adrian E. Roitberg
J. Chem. Theory Comput., 2012, 8 (11), pp 4393–4404
DOI: 10.1021/ct300512h
and/or
Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent
Using Discrete Protonation States: Implementation, Testing, and Validation
Jason M. Swails, Darrin M. York, and Adrian E. Roitberg
J. Chem. Theory Comput., 2014, 10 (3), pp 1341–1352
DOI: 10.1021/ct401042b
The method, as implemented in amber, does the changes in protonation
based in an implicit solvent model, even when the dynamics is done in
explicit solvent. As such the charge change happens in implicit solvent,
which does not suffer the problems of changing charges in explicit
solvent and using PME.
The dynamics is done in explicit solvent, but that part does not care
about the total charge, as long as it does not change. Since each
section of MD is done at constant total charge, there is no problem.
adrian
On 3/22/17 9:33 AM, Elisa Pieri wrote:
> Hello,
>
> in CpHMD, when a residue changes its protonation state, also the net charge
> of the system changes. I would like to know how this is handled from a
> technical point of view. Can you help me?
>
> Thanks!
> Elisa
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Mar 22 2017 - 07:30:03 PDT
