Re: [AMBER] MD simulation at 1M or 2M salt concentration

From: Jason Swails <>
Date: Mon, 29 Sep 2014 08:43:24 -0400

On Mon, Sep 29, 2014 at 8:48 AM, 张后今 <> 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.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Sep 29 2014 - 06:00:05 PDT
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