[gmx-users] large scale simulation?

Oliver Stueker ostueker at gmail.com
Fri Mar 30 23:13:55 CEST 2012

Hi Albert,

With the Information you give here, it's hard to give you specific
advice on how to speed up your simulations.
I found the following papers quite interesting and maybe they give you
some idea in how to improve the performance.

1. Larsson P, Hess B, Lindahl E (2011)
  Algorithm improvements for molecular dynamics simulations.
  Wiley Interdisciplinary Reviews: Computational Molecular Science 1: 93-108.
  Available: http://doi.wiley.com/10.1002/wcms.3

2. Larsson P, Lindahl E (2010)
  A high-performance parallel-generalized Born implementation enabled
by tabulated interaction rescaling.
  Journal of Computational Chemistry 31: 2593-600.
  Available: http://dx.doi.org/10.1002/jcc.21552

3. Bjelkmar P, Larsson P, Cuendet MA, Hess B, Lindahl E (2010)
  Implementation of the CHARMM Force Field in GROMACS: Analysis of
Protein Stability
  Effects from Correction Maps, Virtual Interaction Sites, and Water Models.
  Journal of Chemical Theory and Computation 6: 459-466.
  Available: http://pubs.acs.org/doi/abs/10.1021/ct900549r

On Fri, Mar 30, 2012 at 11:02, Albert <mailmd2011 at gmail.com> wrote:
> Hello:
>   I am wondering does anybody have experience with GROMACS for large scale
> simulation? I've heard lot of people said that it would be difficult for
> Gromacs to do so. eg: I've got a 60,000 atoms system, is it possible for
> GROMACS to produce 100 ns/days or even more? suppose I can use as much CPU
> as possible.... My recent experience for such system, Gromacs can only
> produce up to 20ns/day.... If I would like to produce 1000 ns, I have to
> wait for 50 days......
> thank you very much
> best
> A.

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