From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Sep 27 2012 - 20:13:04 CDT
My initial reaction, in terms of two cents, is that the "error" you are
getting is really small, such that I wouldn't be bothered by that. Also,
what do you mean by "experimental density"? If you mean the density
measured in a lab, then it's hardly surprising that you don't get the same
value, as you are doubtlessly using a model that makes some assumptions.
Unless your simulation is being run with a highly detailed and
polarizable/QM model, I would never expect it to reach the exact density of
those molecules in the lab.
~Aron
On Thu, Sep 27, 2012 at 3:17 PM, Guanglei Cui
<amber.mail.archive_at_gmail.com>wrote:
> Assuming 10ns is long enough for the box to reach equilibrium, I would
> investigate why there is a large difference between the expt and
> calculated values. You may also want to check other bulk properties of
> your system, if they are important to you.
>
> Just my two cents ...
>
> Regards,
> Guanglei
>
> On Thu, Sep 27, 2012 at 8:40 AM, oguz gurbulak <gurbulakoguz_at_yahoo.com>
> wrote:
> > Dear All,
> >
> > I run md simulations in order to equilibrate a box of molecules. The
> target
> > experimental density value is 1.261 g/cm3. But I reached 1.245 g/cm3 for
> > density value after a 10 ns simulation. Can I use these molecules with
> this
> > density value for my initial structure ? or Should I continue to run md
> > simulations to get the experimental density value 1.261 g/cm3 ?
> >
> > Could you please share your thoughts and advice with me ?
> >
> > Thanks for the help.
>
>
>
> --
> Guanglei Cui
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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