A LIBRARY OF SOFTWARE ON MOLECULAR DYNAMICS, MONTE CARLO, LATTICE STATICS AND LATTICE DYNAMICS

CCP5 Program Library Conditions of Distribution

The CCP5 Program Library provides programs and documentation free of charge to academic centres upon application to Dr. W. Smith at this address . For people without a WWW client, a service on anonymous ftp or by E-mail is available. A list of programs available is presented in the following pages. The programs are provided on condition that applicants do not exploit the programs for commercial purposes e.g. for resale or distribution as part or whole of a commercial product.

Readers should also note that we are authorised to supply the example programs originally published in the book ``Computer Simulation of Liquids'', by M.P. Allen and D.J. Tildesley (Clarendon Press, Oxford 1987). These are supplied in the same manner as the resident CCP5 programs. We are grateful to Mike Allen and Dominic Tildesley for their permission. We should also like to remind readers of this page that we would welcome further contributions to the Program Library. The Library exists to provide support for the research efforts of everyone active in computer simulation and to this end we are always pleased to extend the range of software available. If any of our readers have any programs they would like to make available, please would they contact Dr. Smith at this address .

Please Note: For copyright reasons we are not able to supply the programs CASCADE, SYMLAT, THBFIT,THBPHON and THBREL free of charge to Universities outside the United Kingdom.

CONTENTS OF THE LIBRARY

The library is now divided into internal and external links. In some cases a local mirror copy of an external program is kept. The library contents is given in the table below and you may browse the entire directory . The table consists of the program name, a list of flags describing the capabilities of the program and the author. If online documentation exists then the program reference will contain the keywords manual and description of program . For most of the programs there is only paper documentation which may be obtained by writing to Dr. W. Smith at this address . Links to the flags describing the program capabilities refer to an index at the end of the list of contents.

INTERNAL LINKS

Notes

There are two versions of the program CARLOS, CARLOS1 and CARLOS2 .

There are three versions of the program HMDIAT, HMDIAT3 , HMDIAT4 and HMDIAT5 .

There are three test datasets MDCSPC4.DATA05 , MDCSPC4.DATA06A and MDCSPC4.DATA06B .

There are two versions of the program MDIONS, MDIONS1 and MDIONS2 .

There are two versions of the program PIMCLJ, PIMCLJ1 and PIMCLJ2 .

There are two versions of the program SFMK, SFMK1 Description of program and SFMK2 Description of program .

There are two programs SOTON_PAR each with a master and worker file (see description of program), 2sq.master 2sq.worker 3cu.master 3cu.worker .

There are two programs TEQUILA with assorted input files tequila hysteria Datasets 1BP2.PDB 1LZ1.PDB 1P2P.PDB 1PPT.PDB 2LZ2.PDB 2LZM.PDB x2.bkv

EXTERNAL LINKS

DYNAMO

DYNAMO
Author D. Fincham

MOLDY

MD   PRMD   BHM   MIX   GEN   BE   CP   RDF   Description of Program   manual   WWW page   Author K. Refson

MOLDY is available from the ftp server in the Earth sciences Department, Oxford, in several format.

NEMD

MD   LJA   SLLOD   Macintosh   WWW Page   Author D. J. Evans

These are local copies of the two versions of the non-equilibrium molecular dynamics program:

Motorola   PowerPC

SOFTWARE PROVIDED BY MIHALY MEZEI

The links are to M. Mezei's pages
Software MMC: (T,V,N), (T,P,N), (T,V,mu) ensemble Monte Carlo simulations (free energy with polynomial TI, or with Adaptive Umbrella Sampling), Proximity Analysis
Simulaid: simulation setup utilities for optimal solute placement, conversions and analysis, animating trajectories
Intocham: conversion from InsightII to Charmm, Amber or Moil formats
Simloc: detection of local similarities between conformations
Maxwell: multipole expansion for fluid and crystalline phase with the Maxwell formalism
Gibbs: cavity-biased Gibbs ensemble Monte Carlo
Atomc: multi ensemble atomic fluid Monte Carlo

THE MOLECULAR MODELLING TOOLKIT

From Centre de Biophysique Moléculaire
Orléans, France
The Molecular Modelling Toolkit 2.0
Mirror site in USA
The Molecular Modelling Toolkit 1.0
Mirror site in USA

Program types

Properties

System models

Algorithm

``Computer Simulation of Liquids''

Programs from the Book: ``Computer Simulation of Liquids'' by M.P. Allen and D. Tildesley Clarendon Press Oxford 1987.

These programs originally appeared on microfiche in the book ``Computer Simulation of Liquids'' by M. P. Allen and D. J. Tildesley published by Oxford University Press 1987. They are made freely available to members of CCP5 in the hope that they will be useful. The intention is to clarify points made in the text rather than to provide a piece of code suitable for direct use in a research application. We ascribe no commercial value to the programs themselves. Although a few complete programs are provided our aim has been to offer building blocks rather than black boxes. As far as we are aware the programs work correctly but we can accept no responsibility for the consequences of any errors and would be grateful to hear from you if you find any. You should always check out a routine for your particular application. The programs contain some explanatory comments and are written in the main in FORTRAN-77. One or two routines are written in BASIC for use on microcomputers. In the absence of any universally agreed standard for BASIC we have chosen a very rudimentary dialect. These programs have been run on an Acorn model B computer. Hopefully the translation of these programs into more sophisticated languages such as PASCAL or C should not be difficult.

M.P.Allen

Programs from the Book ``Computer Simulation of Liquids''

Availability of the Allen/Tildesley example programs at Cornell

Appendix F of the Book ``Computer Simulation of Liquids'' by M. P. Allen and D. J. Tildesley describes a method whereby the example programs may be obtained from the statistical mechanics group FTP facility at Cornell. This facility is no longer operational as advertised, due to software and hardware changes. However, the programs are still available. To obtain them, the preferred method is now to use anonymous ftp rather than Email, as described below.

You will need to access the ftp server
ftp.cheme.cornell.edu
and look in the directory
allen_tildesley.

CCP5 Program Library E-Mail Service

For people who do not yet have access to WWW, it is possible for CCP5 members to get copies of CCP5 programs through E-mail or anonymous ftp.

Email

To access the library by E-mail send an E-mail message to info-server@dl.ac.uk. The contents of the e-mail message should be as follows (Note: the use of upper and lower case is significant - this is a unix system!): 
request sources
topic index CCP/ccp5
topic CCP/ccp5/program-name
Where program-name is the name of the desired source code. A mail server will automatically process this message and return a copy of the source code to your e-mail address. Please note the following however: The program source will be returned to you in uue format, which is a form of encoding most suitable for mail messages. It can easily be decoded on any unix system using the uudecode command. (Check your local unix man file for details). Also, to speed the transfer, the source will be split into files of 1200 records each, so expect two or three such files for the average CCP5 program. Once again, uudecode will help you to sort things out. Readers who do not have unix facilities should include the following lines at the start of the above message: 
line-limit: nnnnn
coding: off
Where nnnnn is the number of records in the source (in most cases 6000 should be enough). The program will be sent in plain FORTRAN as a single file. It may take a while to arrive, but be patient! Also beware in case your system mailer cannot handle messages of this size. The programs from ``Computer Simulation of Liquids'' are also available. To access them use program-name F.01, for example.

anonymous ftp

The entire CCP5 program library is now accessible by anonymous FTP. The procedure is as shown in the table. 
1.    move to the desired directory on YOUR machine 
2.    type:                                           ftp ftp.dl.ac.uk
3.    enter userid:                                   anonymous 
4.    enter passwd:                                   enter your name and site
5.    change to ccp5 directory:                       cd ccp5 
6.    to list the directory contents:                 ls  
7.    if desired change to lower directory e.g        cd TEQUILA 
8.    to get a compressed file (.Z)                   binary 
9.    to get a single file type:                      get filename  
10    to get multiple files type:                     mget *.* 
11.                                                   quit
Readers must realise that the terms of use and distrubution of the CCP5 programs that have applied hitherto will be maintained. Users should not redistribute or sell the programs, nor is any liability accepted for their use, either by CCLRC or the program authors. It is a requirement on the user that the programs be fully tested for their intended purpose. Any bugs found should be reported to the librarian, for the benefit of other users.
CCLRC CCP5

M. Leslie Written 12 April 94 Last modified 15 February 2000