| |
|
|
|
| |
CHARMM
| Description |
CHARMM (Chemistry at HARvard Macromolecular Mechanics) models the dynamics and mechanics of macromolecular systems using empirical and mixed empirical/quantum mechanical force fields.
CHARMM is designed to investigate the structure and dynamics of large molecules. It performs free energy calculations of mutations and drug binding as well as conformational folding of peptides. It uses classical mechanical methods to investigate potential energy surfaces derived from experimental and "ab initio" quantum chemical calculations. In addition, mixed quantum mechanical/classical systems can be defined to investigate chemical processes such as enzyme catalysis.
Official Homepage
|
| Documentation |
Users Manual
The following documentation is a good starting point for those who begin to work on CHARMM.
Other References
- CHARMM: The Biomolecular simulation Program, J. Comp. Chem. 30, 1545-1615 (2009), by B. R. Brooks, C. L. Brooks III, A. D. Mackerell, L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, and M. Karplus.
- CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, J. Comp. Chem. 4, 187-217 (1983), by B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus.
- CHARMM: The Energy Function and Its Parameterization with an Overview of the Program, in The Encyclopedia of Computational Chemistry, 1, 271-277, P. v. R. Schleyer et al., editors (John Wiley & Sons: Chichester, 1998), by A. D. MacKerell, Jr., B. Brooks,C. L. Brooks, III, L. Nilsson, B. Roux, Y. Won, and M. Karplus.
|
| License Agreement and Citation Format |
License Agreement
Citation Format
CHARMM: The Biomolecular simulation Program, J. Comp. Chem. 30, 1545-1615 (2009), by B. R. Brooks, C. L. Brooks III, A. D. Mackerell, L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, and M. Karplus.
|
| How to Access the Program |
|
Availability
| Server |
Version |
Path |
Parallelization Methods |
| Axle |
34b2 |
/apps/charmm/exec/gnu |
MPI |
|
| Using the Program |
|
charmm - Parallel version
=========================
Usage: mpirun <MPI_OPTIONS> -n <NUM_PROCS> /apps/charmm/exec/gnu/charmm < <CHARMM_INPUT_FILE>
charmm-s - Serial version
=========================
Usage: /apps/charmm/exec/gnu/charmm-s < <CHARMM_INPUT_FILE>
charmm - Parallel version
Usage: mpirun <MPI_OPTIONS> -n <NUM_PROCS> /apps/charmm/exec/gnu/charmm < <CHARMM_INPUT_FILE>
charmm-s - Serial version
Usage: /apps/charmm/exec/gnu/charmm-s < <CHARMM_INPUT_FILE>
|
| Additional Notes |
| |
|
|
Last Updated - 4th Oct 2011 |
|
|
|
