| 1 |
What is OpenMD? |
| 2 |
|
| 3 |
OpenMD is an open source molecular dynamics engine which is capable of |
| 4 |
efficiently simulating liquids, proteins, nanoparticles, interfaces, |
| 5 |
and other complex systems using atom types with orientational degrees |
| 6 |
of freedom (e.g. "sticky" atoms, point dipoles, and coarse-grained |
| 7 |
assemblies). Proteins, zeolites, lipids, transition metals (bulk, flat |
| 8 |
interfaces, and nanoparticles) have all been simulated using force |
| 9 |
fields included with the code. OpenMD works on parallel computers |
| 10 |
using the Message Passing Interface (MPI), and comes with a number of |
| 11 |
analysis and utility programs that are easy to use and modify. An |
| 12 |
OpenMD simulation is specified using a very simple meta-data language |
| 13 |
that is easy to learn. |
| 14 |
|
| 15 |
Simulations are started in OpenMD using a single Molecular Dynamics (.md) |
| 16 |
file. These files must start with the <OpenMD> tag and must |
| 17 |
have two sections: |
| 18 |
|
| 19 |
1) a C-based <MetaData> section, and |
| 20 |
|
| 21 |
2) a <Snapshot> block for initial coordinate and velocity information. |
| 22 |
|
| 23 |
Detailed descriptions of the structures of these files are |
| 24 |
available in the "doc" directory. Sample simulations are |
| 25 |
available in the "samples" directory. |
| 26 |
|
| 27 |
What you need to compile and use OpenMD: |
| 28 |
|
| 29 |
1) Good C++ and C compilers. We've built and tested OpenMD |
| 30 |
on the following architecture & compiler combinations: |
| 31 |
|
| 32 |
Architecture CC CXX Notes |
| 33 |
------------------------- ---- ----- ---------------------- |
| 34 |
ix86-pc-linux-gnu icc icpc (Intel v. 10) |
| 35 |
i386-apple-darwin11.1.0 gcc g++ (GNU v.4.3) |
| 36 |
i386-apple-darwin11.1.0 icc icpc (Intel v. 12) |
| 37 |
x86_64-unknown-linux-gnu gcc g++ (Pathscale 3.2) |
| 38 |
|
| 39 |
2) CMake, a cross-platform build system which is available at |
| 40 |
http://www.cmake.org Most Linux and some Unix distributions |
| 41 |
provide CMake as a standard package. If not, please download it, |
| 42 |
and make sure you get a recent version. Mac OS X users can either |
| 43 |
download the CMake installer or install it from the command line |
| 44 |
using macports. |
| 45 |
|
| 46 |
3) MPI-2 is optional for the single processor version of OpenMD, but |
| 47 |
is required if you want OpenMD to run in parallel. We like |
| 48 |
OpenMPI. Other implementations of MPI-2 might work, but we haven't |
| 49 |
tested them. You can get Open MPI here: http://www.open-mpi.org/ |
| 50 |
|
| 51 |
4) Other optional (but quite useful) libraries that will unlock some |
| 52 |
features of OpenMD: |
| 53 |
|
| 54 |
Open Babel: http://openbabel.org |
| 55 |
Qhull: http://www.qhull.org |
| 56 |
FFTW: http://www.fftw.org |
| 57 |
|
| 58 |
5) Some of the utility scripts depend on Python and Perl. These |
| 59 |
interpreters are common installations on most flavors of Unix and |
| 60 |
Mac OS X. |
| 61 |
|
| 62 |
|
| 63 |
INSTRUCTIONS |
| 64 |
|
| 65 |
1) Get, build, and test the required pieces above. |
| 66 |
2) cmake . |
| 67 |
3) make |
| 68 |
4) make install |
| 69 |
|
| 70 |
That's it. |
