On Wed, Nov 20, 2013 at 2:45 AM, Yip Yew Mun <yipy0005.gmail.com> wrote:
> Hi,
>
> I have read an article entitled “Molecular Dynamics Simulations of Protein
> Folding” by Angel E. Garcia, it’s a Springer article. Inside the article,
> the author plotted 2 graphs: 1) < E > against T, 2) 𝜎 against T in order
> to ascertain whether the chosen temperature range and exchange probability
> work fine. I wish to do the same to my REMD simulations, how can I do it
> with AMBER?
>
Run a short simulation at each temperature, then extract all of the
(potential) energies from the mdout files. Take their average and variance
and plot them vs. temperature (this is what the axes on the plots say was
plotted). As a general note, this has nothing to do with Amber. The above
recipe applies to any temperature REMD simulation run with any MD package.
2) is a little ambiguous, though. Technically sigma is the square root of
the variance (which is the standard deviation), yet the original paper says
he plots the second moment (which is just the variance).
If unable, is there other ways I can check if the temperature range and
> exchange probability that I chosen are working fine?
>
Run a short REMD simulation and check the exchange success rates. If
they're about where you want them, it's likely fine. (20% success is widely
recognized as a good target)
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 20 2013 - 14:30:02 PST
