From: Guanglei Cui (amber.mail.archive_at_gmail.com)
Date: Thu Sep 27 2012 - 14:17:47 CDT
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
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