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

From: Jason Swails <>
Date: Mon, 29 Sep 2014 09:01:11 -0400

On Mon, 2014-09-29 at 08:43 -0400, Jason Swails wrote:
> 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.

Ah, I think I misunderstood your problem. If you added ions, ran
simulations, and saw that many ions moved outside the box, then it is
just an issue of imaging, and Carlos' answer applies.

I thought you used VMD to add ions, and they were placed outside the
solvent box. In that case, we won't be able to provide much help with
that (or at least not as much as the VMD mailing list).

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Sep 29 2014 - 06:30:02 PDT
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