On Tue, Sep 22, 2015 at 5:07 PM, Marcelo Andrade Chagas <
andrade.mchagas.gmail.com> wrote:
> Dear AMBER of the list,
>
> Thanks for the previous answers, I'm evolving.
>
> I got the little conduct a test using the following procedure to achieve
> solvation:
>
> loadamberparams frcmod.iosjc_spce
>
This should be "frcmod.ionsjc_spce" (if you are using SPCE, of course;
otherwise use the one appropriate for your water model).
> solvatebox mol SPCBOX 10
> loadamberparams frcmod.spce
> addions mol Na+ 0
> As I understand it when using the above sequence for now
> other types of water model is only exchange the term
> the corresponding command lines ???
>
Yes.
>
> With this in my file I have added two Na+ ions and the simulation box
> solvated was created.
>
> Now this is right ????
>
This should have added neutralizing counterions. I encourage you to use
ParmEd and use some of the commands to look at the system. For example,
"netCharge :*" will tell you the net charge of the system. "summary" will
give you a breakdown of the amount of solvent, ions, and other types of
residues are in your system. etc.
> As do the same to put solvation via implicit solvent ???
>
implicit solvent doesn't use explicit counterions -- it is accounted for
implicitly through a Debye-like screening parameter.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 22 2015 - 14:30:04 PDT
