[gmx-developers] Use of invsqrt with tables

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 23 13:00:12 CET 2016


In all versions of gromacs the distance between two nonbonded atoms is 
computed as
             rinv00           = gmx_invsqrt(rsq00);
             r00              = rsq00*rinv00;

This is fine when we use Lennard Jones and Coulomb, but not when using 
table potentials which do not necessarily have singularities at r = 0. I 
would therefore propose to replace the statements by a normal sqrt in 
all innerloops using tables.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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