Mindy 1.0

Mindy is a very simple, serial molecular dynamics program derived from NAMD source code. It currently uses xplor parameter and structure files. The program is written in very straightforward C++.

Installation

Unpack the distribution. A directory named "mindy" will be created. In the mindy directory are two subdirectories, "src" and "test". The "src" directory contains the source code and a Makefile to build mindy.

Typing "make" within the src directory shoud build mindy using g++. If you would like to build mindy using a different compiler or different compiler flags, use one of the build targets in the Makefile or add a new one.

The executable is named mindy_$ARCH, where ARCH is the platform. by default, this is "g++".

Using

The command line syntax for mindy is:

mindy nsteps pdbfile psffile paramfile

Nsteps specifies how many timesteps to take. pdbfile and psffile are the coordinate and structure files, respectively, of the system you want to simulate. paramfile is the name of your parameter file. Both the psf file and the parameter must be in X-Plor format.

The test directory contains two sets of files which can be used as inputs for mindy. "alanin" is a 66 atom polypeptide, and "brH" is a crystal structure of bacteriorhodopsin containing 3762 atoms. Run alanin by typing

mindy 1000 alanin.pdb alanin.psf alanin.params

at the command line.