if the ions are "not in the water box", where are they? if outside the box,
and the simulation is periodic, then you probably have not done periodic
imaging on the system. search the archives for many examples.
one thing you will need to check is the concentration of ions after the box
size adjusts (if you are running constant pressure). often the initial box
is larger than the final equilibrated box size.
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?
>
>
> > -----原始邮件-----
> > 发件人: "Jason Swails" <jason.swails.gmail.com>
> > 发送时间: 2014年9月29日 星期一
> > 收件人: amber.ambermd.org
> > 抄送:
> > 主题: Re: [AMBER] MD simulation at 1M or 2M salt concentration
> >
> > On Sun, 2014-09-28 at 09:59 +0800, 张后今 wrote:
> > > Hi, guys:
> > >
> > >
> > > I would like to do simulation with a halophilic enzyme. The optimal
> > > salt concentration for this protein is 2M salt. Is Amber suitable for
> > > this kind of work? I am not sure if the force fields have been tested
> > > at such high salt concentration.
> >
> > This is more a question to ask about a specific set of ion parameters
> > within a force field, not of a piece of software. If you are simulating
> > monovalent salt ions, then the parameters should be pretty good. I
> > would suggest looking into the citations for the different ion
> > parameters provided within Amber and see what they say.
> >
> > Divalent metal ions are a different story. I would recommend looking at
> > chapter 3, section 9 (page 45) in the Amber 14 manual for a more
> > thorough discussion of ion parameters (as well as a list of references
> > to consult for more information).
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Sep 29 2014 - 06:00:06 PDT
