On Mon, Sep 29, 2014 at 8:48 AM, 张后今 <hjzhang.hust.edu.cn> wrote:
> Thank you very much for your swift reply.
>
> We need to simulate sodium chloride which is a monovalent salt. Firstly,
> some Na+ ions were added to neutralize the system. Then, the system was
> solvated. Then, the amount of additional ions was calculated according to
> the water box size before more ions were added into the system. However,
> when we checked the water box in VMD, we found a good portion of the ions
> are not in the water box. This makes the actual concentration of the ions
> smaller than expected.
>
> So how could we add ions to reach the exact concentration?
>
Use tleap. Or ask on the VMD forum.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 29 2014 - 06:00:05 PDT
