Gromacs

Floating Point Arithmetic

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    GROMACS spends its life doing arithmetic on real numbers, often summing many millions of them. These real numbers are encoded on computers in so-called binary floating-point representation. This representation is somewhat like scientific exponential notation (but uses binary rather than decimal), and is necessary for the fastest possible speed for calculations. Unfortunately the laws of algebra only approximately apply to binary floating-point. In part, this is because some real numbers that are represented simply and exactly in decimal (like 1/5=0.2) have no exact representation in binary floating-point, just as 1/3 cannot be represented in decimal. There are many sources you can find with a search engine that discuss this issue more exhaustively, such as Wikipedia.

     

    So, the sum of a large number of binary representations of exact decimal numbers need not equal the expected algebraic or decimal result. Users observe this phenomenon in a few places:

    • sums of partial charges expressed to two decimal places sometimes only approximate the integer total charge to which they contribute (however a deviation in the first decimal place would always be indicative of a badly-formed topology).  When GROMACS has to represent such floating-point numbers in output, it sometimes uses a computer form of scientific notation known as E notation. In such notation, a number like -9.999971e-01 is actually -0.9999971, which is close enough to -1 for purposes of assessing the total charge of a system.
    • when the size of the simulation time step needs six decimal places for its exact representation in units of nanoseconds, the total simulation time in nanoseconds after a million steps need not be exactly an integer

     

    It is also not appropriate for GROMACS to guess to round things, because such rounding relies on assumptions about the inputs that need not be true. Instead the user needs to understand how their tools work.

    Page last modified 06:40, 21 Jun 2011 by mabraham