On Thu, 2015-03-26 at 11:59 +0000, Glenn Carrington [bs10g3c] wrote:
> Thanks very much for the information.
> I initially used the Langevin thermostat as per the AMBER tutorial,
> but it took ages to get 100 steps on the GPU. Switched to Berendsen
> and the GPU simulation ran noticeably faster. I have not got the
> timings to hand, but I'm guessing a x2 speed increase at least.
I find that surprising... The complexity of generating the random
numbers is O(N) (really 3N, with somewhat-expensive logarithms and
trigonometric functions required to convert a uniform distribution into
a normal distribution), and it is all done on the GPU directly. By
contrast, the nonbonded calculation is O(N^2) (times two, since the GB
radii and GB energies must be computed in separate double-loops). For
large systems, the nonbonded loop should completely swamp the time
requirements of the random number generation. Scott -- am I missing
something subtle here?
That said, vrand=1000 isn't a bad setting... That will require ca. 1000x
fewer random numbers than the Langevin integrator (although I still
suspect this is very small compared to the cost of the GB force
calculation).
> However, as mentioned I don't think I can use this thermostat with
> implicit solvent. As the structure has 47,000 atoms, do you think the
> difference between Anderson and Langevin will be more pronounced due
> to the system size?
Andersen and Berendsen should be very similar in terms of computational
cost with a sufficiently large vrand. That said, 47,000 atoms is a
*huge* system to be running with GB... very ambitious.
> I'm hoping so, as the simulation will be painfully slow otherwise.
> Also do you know what is a good setting for vrand?
> I'm not familiar with using nmropt to guide the equilibration temp.
> Hope you don't mind me being cheeky, but could you possibly cut and
> paste a sample of your input file to provide some guidance? Don't
> worry about it if it is inconvenient though.
I have a repository of input files that I put on Github, complete with a
README file that hopefully describes my naming convention:
https://github.com/swails/Mdins
"slow_heat" is the nmropt-controlled temperature variation.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 26 2015 - 07:30:02 PDT
