Mindy 1.0

Mindy is a little molecular dynamics program. Mindy is very simple, serial molecular dynamics program derived from NAMD source code. It currently uses Xplor parameter and structure files. The program is written in C + + very simple. InstallationUnpack distribution. A directory named "Mindy" is created. Mindy in the directory are two subdirectories, "src" and "test". The "src" directory contains the source code and a Makefile to build mindy.Typing "make" in src directory shoud build using g + + Mindy. If you want to build Mindy using a different compiler or different compiler flags, use one of the objectives of building in the Makefile or add a new one.The executable named mindy_ $ ARCH where ARCH is the platform. By default it is "g + +". command line syntax for illicit use is Mindy: Mindy nstep pdbfile paramfileNsteps psffile timesteps specifies how much to take. pdbfile and psffile are coordinates and the structure files, respectively, of the system you want to simulate. paramfile is the name of your parameter file. Both the PSF and the file parameter must be in X-Plor format. The test directory contains two sets of files that can be used as inputs for Mindy. "alanine" is a polypeptide 66 atom, and BRH is a crystal structure of bacteriorhodopsin containing 3762 atoms. Alanine run by typing Mindy 1000 alanin.paramsat alanin.psf alanin.pdb the command line.