# General tips

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this page is still a work in progress
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Here is a list of general ideas for improving simulation performance.
Most of them are only applicable to certain models and certain
bottlenecks in the current performance, so let the timing data you
generate be your guide. It is hard, if not impossible, to predict how
much difference these options will make, since it is a function of
problem size, number of processors used, and your machine. There is no
substitute for identifying performance bottlenecks, and trying out
various options.

-   rRESPA
-   Two-FFT PPPM
-   Staggered PPPM
-   single vs double PPPM
-   partial charge PPPM
-   verlet/split run style
-   processor command for proc layout and numa layout
-   load-balancing: balance and fix balance

Two-FFT PPPM, also called *analytic differentiation* or *ad* PPPM, uses
2 FFTs instead of the 4 FFTs used by the default *ik differentiation*
PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
achieve the same accuracy as 4-FFT PPPM. For problems where the FFT cost
is the performance bottleneck (typically large problems running on many
processors), 2-FFT PPPM may be faster than 4-FFT PPPM.

Staggered PPPM performs calculations using two different meshes, one
shifted slightly with respect to the other. This can reduce force
aliasing errors and increase the accuracy of the method, but also
doubles the amount of work required. For high relative accuracy, using
staggered PPPM allows one to half the mesh size in each dimension as
compared to regular PPPM, which can give around a 4x speedup in the
kspace time. However, for low relative accuracy, using staggered PPPM
gives little benefit and can be up to 2x slower in the kspace time. For
example, the rhodopsin benchmark was run on a single processor, and
results for kspace time vs. relative accuracy for the different methods
are shown in the figure below. For this system, staggered PPPM (using ik
differentiation) becomes useful when using a relative accuracy of
slightly greater than 1e-5 and above.

![image](JPG/rhodo_staggered.jpg){.align-center}

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Using staggered PPPM may not give the same increase in accuracy of
energy and pressure as it does in forces, so some caution must be used
if energy and/or pressure are quantities of interest, such as when using
a barostat.
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