Re: [AMBER] Implicit solvent simulation with Andersen thermostat

From: Ross Walker <>
Date: Thu, 26 Mar 2015 08:57:17 -0700

On another note there is a known bug right now with the Anderson thermostat.

It will give incorrect behavior if ntpr >= vrand - so make sure you set ntpr to less than vrand. I have a fix for it but have not yet had time to test it.

> On Mar 26, 2015, at 7:25 AM, Jason Swails <> wrote:
> 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:
> "slow_heat" is the nmropt-controlled temperature variation.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Mar 26 2015 - 09:00:05 PDT
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