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Manuscript Title: SIMLYS: a software package for trajectory analysis of molecular dynamics simulations.
Authors: P. Kruger, M. Luke, A. Szameit
Program title: SIMLYS
Catalogue identifier: ABZD_v1_0
Distribution format: gz
Journal reference: Comput. Phys. Commun. 62(1991)371
Programming language: Fortran.
Computer: VAX.
Operating system: VMS, UNIX, MS-DOS, CROMIX.
RAM: 420K words
Word size: 8
Keywords: Biology, Solid state physics, Other, Trajectory analysis, Molecular dynamics Simulation, Simulation polymer Analysis.
Classification: 3, 7.7.

Nature of problem:
The trajectories of molecular dynamics simulations are generally saved in form of atomic coordinates. Using the coordinates and velocities static and dynamic quantities can be calculated, as for example positional differences, fluctuations or a time series of angle movements.

Solution method:
SIMLYS subdivides the analysis into modules in order to prepare the coordinates and to perform the calculation. A program kernel includes a number of features to provide the selection of the coordinates and to supply the subroutines with required input. Analysis functions are initiated by a command interpreter and perform the calculation by using selected atoms and steps of the simulation. To enable flexibility analysis subroutines can be added and the command language calling the routines can be extended.

Restrictions:
SIMLYS is written in standard FORTRAN-77, to be as transferable as possible. The only exception is the use of the "INCLUDE" statement which can be adapted by using a preprocessor program. It is recommended to use a machine allowing file extensions , because SIMLYS uses default extensions for various files. The current version is installed for 300 atoms and can still be run on an IBM-XT or compatible PC, with 640 Kb memory. The number of atoms can be enlarged as far as storage capacity is available.