Moldy User s Manual Revision 2 16 for release 2 13 Keith Refson Department of Earth Sciences Parks Road Oxford OX1 3PR keith earth ox ac uk January 29 1998 Copyright c 1988 1993 1996 Keith Refson Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies Permission is granted to copy and distribute modified versions of this manual under the conditions for verbat
Smoldyn User s Manual for Smoldyn version 2 38 October 2015 Steve Andrews Part I User s manual 1 1 Overview of Smoldyn 2 2 Installing Smoldyn 4 3 Using Smoldyn 9 3 1 Running Smoldyn 9 3 2 The configuration file 11 3 3 Space and time 15 3 4 Molecules 19 3 5 Graphics 25 3 6 Runtime commands 29 3 7 Surfaces 34 3 8 Reactions 43 3 9 Compartments 64 3 10 Simulation settings 67 3 11 Ports 69 3 12 Rule based network generation 70 3 13 Filaments 71 3 14 Hybri