Hi George,
You don't necessarily have to "differentiate" between the two as far as
having different "mdin" files, but it's an important distinction to make.
The "equilibration" phase is typically not included when snapshots are used
to calculate thermodynamic and/or statistical data about the system. What I
typically do is run straight production runs after heating, but discard the
beginning 1 or 2 ns of my simulation when I start calculating
statistics/thermodynamics. However, differentiating between them explicitly
helps reinforce the idea that an equilibration phase is necessary and that
those frames are not included in the final analysis.
Others may have more to add/comment on.
Hope this helps,
Jason
On Wed, Aug 25, 2010 at 2:46 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi
>
> It is stated in the tutorial (Section 2:
> http://ambermd.org/tutorials/advanced/tutorial3/section2.htm) that "the
> production phase of the simulation should be run using the same conditions
> as the final phase of equilibration to prevent an abrupt jump in the
> potential energy due to a change in simulation conditions". Indeed, the
> prod.in file differs from the equil.in file in only the number of steps
> the coordinates are written to the mdcrd and the number of steps energy
> information is printed to mdout and mdinfo.
>
> My question may seem trivial but why differentiate between the last stage
> of equilibration and production?
>
> Have I missed something?
>
> Best regards
>
> George
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Aug 25 2010 - 04:30:06 PDT
