[gmx-users] Constraints and efficency

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 5 22:28:44 CET 2011

On 2011-01-05 21.44, Elton Carvalho wrote:
> On Tue, Jan 4, 2011 at 7:38 PM, Mark Abraham<Mark.Abraham at anu.edu.au>  wrote:
>> On 5/01/2011 5:53 AM, Elton Carvalho wrote:
>>> [...] Does the larger timestep allowed by eliminating
>>> high-frequency O-H vibrations outweigh the time needed by SETTLE?
>> Most definitely. Typical GROMACS simulations report up to a few percent of
>> the total simulation time is spent in dealing with constraints. If the use
>> of constraints permitted a 2fs timestep rather than 0.5fs, then it's nearly
>> a four-fold speed-up.
> Thanks :)
> So, the larger ts allowed would be indeed the main reason to apply
> constraints...

No! Harmonic bonds are not good either. This is described in chapter 1 
of the manual.

>>> Any other reason I failed to notice?
>> I seem to recall that bond constraints are held to model the essential QM
>> nature of interatomic bonds better than a Morse or harmonic potential
>> (particularly for bonds to hydrogen). I don't recall a reference for that
>> offhand, unfortunately. Perhaps the original SHAKE paper.
> Ok, I'll take a look at those papers, thank you
>>> The only reason I see to constrain movement other than that fraquency
>>> shaving (and, of course, isolating some behaviour of interest, but
>>> this is case-specific) would be to reduce the number of dimensions of
>>> the phase space and save computatuon time, but, as implemented, this
>>> doesn't seem possible with the code as is.
>> Various coarse-graining approaches exist to take advantage of that kind of
>> saving, but they also gain from the higher maximum time step.
> Oh, yes, coarse-graining methods definitely reduce the complexity of
> the system, but I was focusing on all-atom simulations in my message.
> Again, thank you for your response,
> Best regards,

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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