Re: actual production MD

From: Oscar Bastidas (
Date: Tue May 05 2020 - 14:44:50 CDT

It is an actual technical run for namd. What will happen is that the
configuration file that has the line of code for minimization will produce
output (say, the dcd trajectory file) that will contain snapshots of your
protein equilibrating as well as the motions of the protein after such
equilibration (these post-equilibration dynamics are what you want to
analyze for study of your protein). Please keep in mind the order of
events are: minimization, equilibration and finally, actual production.
It's important to note that in this particular conf file, you have to
specify a simulation time length that will be long enough for you to
observe both the equilibration phase and the actual dynamics you care
about. The tutorial you refer to should have (at least the older version I
learned from has it) a section on how you can summon a plot of, say RMSDs
(I think it's using VMD), and if your simulation time is long enough, then
you should see the graph rising and then plateauing. The rising region is
your protein equilibrating (what you don't care about) and the plateau
region is your actual protein simulation data (what you do care about).
Lastly I'll add that the aforementioned graph does not capture the
minimization. Those minimization results remain hidden in the
aforementioned dcd file and RMSD plotting to my knowledge. Once you see
you're in the plateau region, you can then use those results as input to
subsequent simulations and those results can then be treated as your actual
protein dynamics fluctuation data without having to worry about ignoring
the rising/equilibration region.

Hope this helps.


On Tue, May 5, 2020, 7:47 AM L- <> wrote:

> Any kind of suggestions are highly appreciated.
> On Tue, May 5, 2020 at 4:02 AM L- <> wrote:
>> Dear NAMD
>> I need your to help to understand :
>> if I flow the NAMD TUTORIAL minimization-equilibration simulation is
>> this an actual production MD?
>> I mean to run the configuration file for minimization-equilibration is
>> simulation?
>> or I need to run quench to sample the structural characteristics and
>> dynamics?
>> Many thanks

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