From: Jrme Hnin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri Mar 25 2011 - 06:25:30 CDT
Hi Ajasja,
It's hard to have a gut feeling when you didn't tell us anything about
your system. As a comparison though, remember that people who do
umbrella sampling would probably chop up this space into at least a
hundred windows, and suffer any convergence problems that would arise.
The difference is, they would have no other choice (besides
relinquishing umbrella sampling entirely). So whatever you end up
doing, you can find comfort in the fact that it's better than umbrella
sampling.
Anyway, the questions are: are there degrees of freedom other than
your RCs that can get stuck? (hint: the answer is yes) and then: how
much do the RCs have to move about to give those a chance to get
unstuck (and how long will it take)? That should give you an idea of a
minimum size for the quadrants, and a minimum sampling time for each
of them (of course that can and should be adjusted by monitoring
relaxation in the simulations).
Cheers,
Jerome
On 25 March 2011 10:52, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com> wrote:
> Dear all,
> Is there any advisable limit on how many quadrants a 2D torsional free
> energy scan using ABF can be divided? Scaling the simulation by splitting
> the ABF calculation has the advantage that each part runs independently, so
> there are no scaling issues.
> On the other hand one is wary of introducing artifacts by the artificial
> wall constraints (as in figure 6b in [1]).
> I'm asking because over the weekend I will have access to 512 cores. My
> simulation has 16.000 atoms, so just throwing more cores at it will not be
> very effective. (I will of course run the necessary scaling benchmarks
> before I start)
> Currently I'm spliting the ABF calculation into 8 parts. Would 36 parts be
> too much? This would then be pieces of 6x6 points.(The bin width is 10
> degrees and the range form -180 to 180).
> I know this strongly depends on the system, but I'm asking for the "gut"
> feeling:)
> Thank you & best regards,
> Ajasja Ljubetič,
> Young reasercher,
> Laboratory of biophysics,
> Institute Jožef Štefan,
> Ljubljana, Slovenia
>
> Christophe Chipot and Jérome Hénin, “Exploring the free-energy landscape
> of a short peptide using an average force,” The Journal of Chemical Physics
> 123, no. 24 (2005): 244906.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:49 CST