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Introduction
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++.
Contact
If you have questions please send email to the author Justin Gullingsrud,
at justin@ks.uiuc.edu
Download
License
Same terms as NAMD license
Documentation
-- Mindy: a "minimal" molecular dynamics program
-- Version 1.0
Mindy is a very simple, serial molecular dynamics program derived
from NAMD source code. It's currently uses xplor parameter and
structure files. The program is written in very straightforward
C++.
**** How to build:
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++".
**** How to run:
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.
**** Where to go from here:
At the top of the source file Integrator.C, you'll find three #define's
that set the cutoff parameters for the simulation. You'll have to recompile
mindy after changing these values.
Mindy does essentially everything that NAMD does, without all the complications
that come with writing a scalable parallel program. It uses the same force
field, file formats, and essentially the same integrator. As such, for people
just beginning molecular dynamics simulations, it's a good way to understand
what's going on "under the hood". NAMD's source code is freely available,
so if you found tinkering with mindy worthwhile, you might have even more
fun messing with the program that inspired it...
Happy simulating.
Justin Gullingsrud
justin@ks.uiuc.edu
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