[gmx-developers] Re: Various integrator questions

Michel Cuendet michel.cuendet at epfl.ch
Thu Aug 11 14:05:09 CEST 2005

David said :

>>M. Marchi, P. Procacci
>>/Coordinates Scaling and Multiple Time Step Algorithms for Simulation of 
>>Solvated proteins in the NPT ensemble/
>>J. Chem. Phys., 109, 5194 (1998)
>If we use a proper multiple time step algorithm which still allows 2-4
>fs time-steps for the non-bonded interactions we can of course make much
>better scaling algorithms. It is trivial to spread the bonded
>interactions over parallel computers, if we don't need constraint
>algorithms parallellization will be much easier.

Hi. The reason I cite the paper above is not really because of the 
multiple timestep feature. It was rather because it gives nice insights 
about an atomic scheme with constraints, and the atomic vs. molecuar 
scaling issue. From the abstract :

" Constant^ pressure and temperature algorithms have been derived based 
on a^ reversible multiple time step (/r/-RESPA) approach and a new 
modification^ of the particle mesh Ewald method. As such they provide^ 
very fast and accurate tools for simulation of complex molecular^ 
systems in ensembles other than the microcanonical. We have also^ 
developed a novel scaling scheme named atomic group scaling which^ is 
similar to atomic scaling, but has important computational advantages^ 
when used in conjunction with bond constraints. The investigation of^ 
the molecular and atomic group scaling schemes against static and^ 
dynamic properties of a test system (a solvated bovine pancreatic^ 
trypsin inhibitor) has confirmed their equivalence also for large 
molecules^ such as proteins"

The built-in multiple-time step ability comes as an extra very nice 
feature of the the RESPA-like integrators. It is directly linked to the 
Trotter expansion of the Liouvilean in successive independent update 
operations. Multiple-time step would also be an excellent thing to have 
in gromacs !



Michel Cuendet, Ph.D. student
Laboratory of Computational Biochemistry and Chemistry
Swiss Federal Institute of Technology in Lausanne (EPFL)
CH-1015 Lausanne						
Switzerland                            Phone : +41 21 693 0324
lcbcpc21.epfl.ch/~mitch	                       +41  1 633 4194

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