Mindy is a molecular dynamics software that operates with minimal features.
Mindy is an efficient molecular dynamics software that has been derived from NAMD source code. It is a simple program, and it currently uses xplor parameter and structure files. Mindy is written in C++, which makes it easy to use and understand.
Installation of Mindy is a straightforward process. You need to unpack the distribution and create a directory named "mindy." Within this directory, you will find two subdirectories, "src" and "test." The "src" directory contains the source code and a Makefile to build the Mindy program. You can build Mindy by typing "make" within the src directory. You can also use different build targets or add new ones to use a different compiler or compiler flags. The executable generated will be named mindy_$ARCH, where ARCH denotes the platform, which is "g++" by default.
Using Mindy is very easy. You need to specify the desired number of timesteps to take by using "nsteps." The "pdbfile" and "psffile" options are used for specifying the coordinate and structure files of the system you want to simulate, respectively. Finally, you need to provide the name of the parameter file by using the "paramfile" option. Both the psf file and the parameter must be in X-Plor format.
The test directory contains two sets of files, "alanin" and "brH," that can be used as inputs for Mindy. "alanin" is a 66-atom polypeptide, and "brH" is a crystal structure of bacteriorhodopsin containing 3762 atoms. To run alanin, you need to type "mindy 1000 alanin.pdb alanin.psf alanin.params" at the command line. Overall, Mindy is a simple and efficient molecular dynamics software that is easy to install and use.
Installation of Mindy is a straightforward process. You need to unpack the distribution and create a directory named "mindy." Within this directory, you will find two subdirectories, "src" and "test." The "src" directory contains the source code and a Makefile to build the Mindy program. You can build Mindy by typing "make" within the src directory. You can also use different build targets or add new ones to use a different compiler or compiler flags. The executable generated will be named mindy_$ARCH, where ARCH denotes the platform, which is "g++" by default.
Using Mindy is very easy. You need to specify the desired number of timesteps to take by using "nsteps." The "pdbfile" and "psffile" options are used for specifying the coordinate and structure files of the system you want to simulate, respectively. Finally, you need to provide the name of the parameter file by using the "paramfile" option. Both the psf file and the parameter must be in X-Plor format.
The test directory contains two sets of files, "alanin" and "brH," that can be used as inputs for Mindy. "alanin" is a 66-atom polypeptide, and "brH" is a crystal structure of bacteriorhodopsin containing 3762 atoms. To run alanin, you need to type "mindy 1000 alanin.pdb alanin.psf alanin.params" at the command line. Overall, Mindy is a simple and efficient molecular dynamics software that is easy to install and use.
What's New
Version 1.0: N/A