How to Cite NAMD

The NAMD License Agreement specifies that any reports or published results obtained with NAMD shall acknowledge its use and credit the developers as:

"NAMD was developed by the Theoretical Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign."

Laxmikant Kalé, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten. NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics, 151:283-312, 1999. abstract

http://www.ks.uiuc.edu/Research/namd/

Papers About NAMD

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé, Robert Skeel, Klaus Schulten, and Richard Kufrin. MDScope---A visual computing environment for structural biology. In S.N. Atluri, G. Yagawa, and T.A. Cruse, editors, Computational Mechanics 95, volume 1, pages 476-481, 1995. abstract

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé, Robert Skeel, Klaus Schulten, and Richard Kufrin. MDScope---A visual computing environment for structural biology. Computational Physics Communications, 91:111-134, 1995. abstract

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé, Robert D. Skeel, and Klaus Schulten. NAMD---A parallel, object-oriented molecular dynamics program. International Journal of Supercomputer Applications and High Performance Computing, 10:251-268, 1996. abstract

L. V. Kalé, M. Bhandarkar, R. Brunner, N. Krawetz, J. Phillips, and A. Shinozaki. NAMD: A Case Study in Multilingual Parallel Programming. In Z. Li, P.-C. Yew, S. Chatterjee, C.-H. Huang, P. Sadayappan, and D. Sehr, editors, Languages and Compilers for Parallel Computing, Lecture Notes in Computer Science, 1366:367-381, 1998. Springer-Verlag. abstract, postscript

James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind Bhandarkar, Neal Krawetz, Laxmikant Kalé, Robert D. Skeel, and Klaus Schulten. Avoiding algorithmic obfuscation in a message-driven parallel MD code. In P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, and R.D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas, Lecture Notes in Computational Science and Engineering, 4:472-482, 1999. Springer-Verlag. abstract

Robert Brunner, Laxmikant Kalé, and James Phillips. Flexibility and Inter-operability in a Parallel Biomolecular Dynamics Code. In M.E. Henderson, C.R. Anderson, and S.L. Lyons, editors, Object Oriented Methods for Interoperable Scientific and Engineering Computing, Proceedings in Applied Mathematics 99, 1999.

Laxmikant Kalé, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten. NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics, 151:283-312, 1999. abstract

R. Sharma, M. Zeller, V. I. Pavlovic, T. S. Huang, Z. Lo, S. Chu, Y. Zhao, J. Phillips, and K. Schulten. Speech/Gesture Interface to a Visual Computing Environment. IEEE Computer Graphics and Applications, March/April 2000, 29-37.

Robert K. Brunner, James C. Phillips, Laxmikant V. Kalé. Scalable Molecular Dynamics for Large Biomolecular Systems. Conferencedings of the IEEE/ACM SC2000 Conference. IEEE Press, 2000. Technical Paper 271. abstract, pdf

James C. Phillips, Gengbin Zheng, Sameer Kumar, and Laxmikant V. Kalé. NAMD: Biomolecular Simulation on Thousands of Processors. Proceedings of the IEEE/ACM SC2002 Conference. IEEE Press, 2002. Technical Paper 277. abstract, pdf

Papers Citing NAMD

Humphrey, W., Bamberg, E., Schulten, K., "Photoproducts of bacteriorhodopsin mutants: A molecular dynamics study," Biophys. J., 72:1347-1356 , 1997.

Izrailev, S., Stepaniants, S., Balsera, M., Oono, Y., Schulten, K., "Molecular dynamics study of unbinding of the avidin-biotin complex," Biophys. J., 72:1568-1581 , 1997.

Bishop, T.C., Kosztin, D., Schulten, K., "How hormone receptor DNA binding affects nucleosomal DNA: The role of symmetry," Biophys. J., 72:2056-2067 , 1997.

Kosztin, D., Bishop, T.C., Schulten, K., "Binding of the estrogen receptor to DNA. The role of waters," Biophys. J., 73:557-570 , 1997.

Bishop, T.C., Skeel, R.D., Schulten, K., "Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics," J. Comput. Chem., 18:1785-1791 , 1997.

Phillips, J.C., Wriggers, W., Li, Z.G., Jonas, A., Schulten, K., "Predicting the structure of apolipoprotein A-1 in reconstituted high-density lipoprotein disks," Biophys. J., 73:2337-2346 , 1997.

Stepaniants, S., Izrailev, S., Schulten, K., "Extraction of lipids from phospholipid membranes by steered molecular dynamics," J. Mol. Model., 3:473-475 , 1997.

Lu, H., Isralewitz, B., Krammer, A., Vogel, V., Schulten, K., "Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation," Biophys. J., 75:662-671 , 1998.

Humphrey, W., Lu, H., Logunov, I., Werner, H.J., Schulten, K., "Three electronic state model of the primary phototransformation of bacteriorhodopsin," Biophys. J., 75:1689-1699 , 1998.

Ben-Nun, M., Molnar, F., Lu, H., Phillips, J.C., Martinez, T.J., Schulten, K., "Quantum dynamics of the femtosecond photoisomerization of retinal in bacteriorhodopsin," Faraday Discuss., Issue 110, 447-462 , 1998.

Kosztin, D., Izrailev, S., Schulten, K., "Unbinding of retinoic acid from its receptor studied by steered molecular dynamics," Biophys. J., 76:188-197 , 1999.

Krammer, A., Lu, H., Isralewitz, B., Schulten, K., Vogel, V., "Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch," Proc. Natl. Acad. Sci. U. S. A., 96:1351-1356 , 1999.

Sheldahl, C., Harvey, S.C., "Molecular dynamics on a model for nascent high-density lipoprotein: Role of salt bridges," Biophys. J., 76:1190-1198 , 1999.

Kale, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K., Schulten, K., "NAMD2: Greater scalability for parallel molecular dynamics," J. Comput. Phys., 151:283-312 , 1999.

Schlick, T., Skeel, R.D., Brunger, A.T., Kale, L.V., Board, J.A., Hermans, J., Schulten, K., "Algorithmic challenges in computational molecular biophysics," J. Comput. Phys., 151:9-48 , 1999.

Lu, H., Schulten, K., "Steered molecular dynamics simulations of force-induced protein domain unfolding," Proteins, 35:453-463 , 1999.

Wolff, D., Rudd, W.G., "Tabulated potentials in molecular dynamics simulations," Comput. Phys. Commun., 120:20-32 , 1999.

Lu, H., Schulten, K., "Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interpret atomic force microscopy observations," Chem. Phys., 247:141-153 , 1999.

Bryant, Z., Pande, V.S., Rokhsar, D.S., "Mechanical unfolding of a beta-hairpin using molecular dynamics," Biophys. J., 78:584-589 , 2000.

Heath, M.T., Dick, W.A., "Virtual prototyping of solid propellant rockets," Comput. Sci. Eng., 2:21-32 , 2000.

Jung, B., Lenhof, H.P., Muller, P., Rub, C., "Simulating synthetic polymer chains in parallel," Futur. Gener. Comp. Syst., 16:513-522 , 2000.

Heffelfinger, G.S., "Parallel atomistic simulations," Comput. Phys. Commun., 128:219-237 , 2000.

Jung, B., Lenhof, H.P., Muller, P., Rub, C., "Simulating synthetic polymer chains in parallel," Lecture Notes In Computer Science, 1593:13-22 , 1999.

Izaguirre, J.A., Catarello, D.P., Wozniak, J.M., Skeel, R.D., "Langevin stabilization of molecular dynamics," J. Chem. Phys., 114:2090-2098 , 2001.

Baudry, J., Tajkhorshid, E., Molnar, F., Phillips, J., Schulten, K., "Molecular dynamics study of bacteriorhodopsin and the purple membrane," J. Phys. Chem. B, 105:905-918 , 2001.

Gullingsrud, J., Kosztin, D., Schulten, K., "Structural determinants of MscL gating studied by molecular dynamics simulations," Biophys. J., 80:2074-2081 , 2001.

Cherepanov, D.A., Mulkidjanian, A.Y., "Proton transfer in Azotobacter vinelandii ferredoxin I: entatic Lys84 operates as elastic counterbalance for the proton- carrying Asp15," Biochim. Biophys. Acta-Bioenerg., 1505:179-184 , 2001.

Isralewitz, B., Baudry, J., Gullingsrud, J., Kosztin, D., Schulten, K., "Steered molecular dynamics investigations of protein function," J. Mol. Graph., 19:13-25 , 2001.

Straatsma, T.P., McCammon, J.A., "Load balancing of molecular dynamics simulation with NWChem," IBM Syst. J., 40:328-341 , 2001.

Wang, Z.Q., Lupo, J.A., Patnaik, S., Pachter, R., "Large scale molecular dynamics simulations of a 4-n-pentyl-4 '- cyanobiphenyl (5CB) liquid crystalline model in the bulk and as a droplet," Comput. Theor. Polym. Sci., 11:375-387 , 2001.

Zhu, F.Q., Tajkhorshid, E., Schulten, K., "Molecular dynamics study of aquaporin-1 water channel in a lipid bilayer," FEBS Lett., 504:212-218 , 2001.

Gao, M., Lu, H., Schulten, K., "Simulated refolding of stretched titin immunoglobulin domains," Biophys. J., 81:2268-2277 , 2001.

Koumanov, A., Karshikoff, A., Friis, E.P., Borchert, T.V., "Conformational averaging in pK calculations: Improvement and limitations in prediction of ionization properties of proteins," J. Phys. Chem. B, 105:9339-9344 , 2001.

Bhandarkar, M.A., Kale, L.V., "A parallel framework for explicit FEM," Lecture Notes In Computer Science, 1970:385-394 , 2001.

Dixit, S.B., Chipot, C., "Can absolute free energies of association be estimated from molecular mechanical simulations? The biotin-streptavidin system revisited," J. Phys. Chem. A, 105:9795-9799 , 2001.

Jensen, M.O., Tajkhorshid, E., Schulten, K., "The mechanism of glycerol conduction in aquaglyceroporins," Structure, 9:1083-1093 , 2001.

Gumbiowski, K., Cherepanov, D., Muller, M., Panke, O., Promto, P., Winkler, S., Junge, W., Engelbrecht, S., "F-ATPase: Forced full rotation of the rotor despite covalent cross-link with the stator," J. Biol. Chem., 276:42287-42292 , 2001.

Skeel, R.D., Hardy, D.J., "Practical construction of modified Hamiltonians," SIAM J. Sci. Comput., 23:1172-1188 , 2001.

Huber, T., Rajamoorthi, K., Kurze, V.F., Beyer, K., Brown, M.F., "Structure of docosahexaenoic acid-containing phospholipid bilayers as studied by H-2 NMR and molecular dynamics simulations," J. Am. Chem. Soc., 124:298-309 , 2002.

Mazevet, S., Collins, L.A., Kress, J.D., "Evolution of ultracold neutral plasmas," Phys. Rev. Lett., 8805:art. no.-055001 , 2002.

Cates, M.S., Teodoro, M.L., Phillips, G.N., "Molecular mechanisms of calcium and magnesium binding to parvalbumin," Biophys. J., 82:1133-1146 , 2002.

Krammer, A., Craig, D., Thomas, W.E., Schulten, K., Vogel, V., "A structural model for force regulated integrin binding to fibronectin's RGD-synergy site," Matrix Biol., 21:139-147 , 2002.

Damjanovic, A., Kosztin, I., Kleinekathofer, U., Schulten, K., "Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics, quantum chemistry, and polaron model study," Phys. Rev. E, 65:art. no.-031919 , 2002.

Kosztin, I., Bruinsma, R., O'Lague, P., Schulten, K., "Mechanical force generation by G proteins," Proc. Natl. Acad. Sci. U. S. A., 99:3575-3580 , 2002.

Lakshminarasimhulu, P., Madura, J.D., "A cell multipole based domain decomposition algorithm for molecular dynamics simulation of systems of arbitrary shape," Comput. Phys. Commun., 144:141-153 , 2002.

Skeel, R.D., Tezcan, I., Hardy, D.J., "Multiple grid methods for classical molecular dynamics," J. Comput. Chem., 23:673-684 , 2002.

Tajkhorshid, E., Nollert, P., Jensen, M.O., Miercke, L.J.W., O'Connell, J., Stroud, R.M., Schulten, K., "Control of the selectivity of the aquaporin water channel family by global orientational tuning," Science, 296:525-530 , 2002.