From: Ganesh Kamath (gkamath9173_at_gmail.com)
Date: Thu Sep 27 2012 - 20:52:16 CDT
What force field are you using? Normally density calculations converge
within 2 to 5 ns.
On Sep 27, 2012 8:14 PM, "Aron Broom" <broomsday_at_gmail.com> wrote:
> 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.
> 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 ...
>> On Thu, Sep 27, 2012 at 8:40 AM, oguz gurbulak <gurbulakoguz_at_yahoo.com>
>> > Dear All,
>> > I run md simulations in order to equilibrate a box of molecules. The
>> > 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
>> > 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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