Re: [AMBER] Implicit solvent simulation with Andersen thermostat

From: Jason Swails <>
Date: Thu, 26 Mar 2015 10:25:55 -0400

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

> 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:

"slow_heat" is the nmropt-controlled temperature variation.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Mar 26 2015 - 07:30:02 PDT
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