I see…
From looking at the plot, I was under the impression that the SMD code worked well, and the problem appeared only in the analysis from CPPTRAJ. Isn’t that true? Or what “supposed” and “output” actually mean?
Gustavo Seabra
> Em 7 de dez de 2015, à(s) 17:14, Jason Swails <jason.swails.gmail.com> escreveu:
>
> On Mon, Dec 7, 2015 at 2:38 PM, Gustavo Seabra <gustavo.seabra.gmail.com>
> wrote:
>
>> 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
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Dec 07 2015 - 18:00:03 PST
