mn2 at hw.ac.uk
Thu May 26 20:51:46 CEST 2005
Thanks for your very informative reply. What sort of contraint is normally
> M.Naser wrote:
>> Hi All,
>> Is there any trick for improving the performance of a lam/mpi parallel
> No, except waiting for the next version which should have a completely
> overhauled parallelization scheme.
>> I am aware of the flags : sort. shuffle and load.
> You write full precision out coordinates, velocities and forces
> (nstxout, nstvout, nstfout) every 100 steps (0.1 with your 1 fs
> timestep). It may be that writing this amount of data to disk is the
> limiting step in your case, and in any case it seems you are wasting
> disk-space (although that may not be a problem for you...).
> In general, full precision x and v are required only for making
> re-starts, for nearly all analysis purposes, the reduced precision
> coordinates (nstxtcout) will be good enough!
> Most people use a 2 fs timestep and constraints (like David suggested),
> and set nstxout and nstvout to something like 10000; nstfout you can set
> to zero.
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