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 <[email protected]> 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. > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
