Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] abzd_v2_0.gz(545 Kbytes)|
|Manuscript Title: SIMLYS version 2.0: A software package for trajectory analysis of molecular dynamics simulations.|
|Authors: P. Kruger, A. Szameit|
|Program title: SIMLYS 2.0|
|Catalogue identifier: ABZD_v2_0|
Distribution format: gz
|Journal reference: Comput. Phys. Commun. 72(1992)265|
|Programming language: Fortran.|
|Operating system: VMS, MS-DOS, UNIX, VM/CMS, CROMIX.|
|RAM: 506K words|
|Keywords: Biology, Solid state physics, Other, Trajectory analysis, Molecular dynamics Simulation, Simulation polymer Analysis.|
|Classification: 3, 7.7.|
Nature of problem:
Simulation techniques are used to generate coordinates. These coordinates can be the result of a molecular dynamics or Monte Carlo simulation or a distance geometry calculation. They are the basis for current trajectory analysis.
SIMLYS is a program with several modules to analyse the coordinates. It has an interface to handle the data and a number of separate modules to perform the analysis. The modular program organisation allows to extend the system with new modules. It uses a command language to initiate the functions.
Reasons for new version:
Several new analysis modules were added, as for instance the calculation of accessible surface areas, nearest neighbours and correlation functions. Existing modules (HBOND, GENHYD) were improved, while other modules (AVMOL, MERGE) were completely replaced. The command interpret- er was revised and the system was made more robust. The complete function to generate and include new pool routines is now available. A number of details were improved as for example the output listings. The machine readable program manual was updated and extended and is included in the copy.
With all modules linked, simulations with 70 atoms maximum are possible on an IBM-PC (640K). This is much less than in version 1.0. If more atoms are to be handled, the number of modules can be reduced. On other machines the size of the system can be increased according to the storage capacity available.
|Disclaimer | ScienceDirect | CPC Journal | CPC | QUB|