NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers. An object-oriented design imple mented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decom position coupled with a multithreaded, message-driven design, which is shown to scale efficiently to multiple processors. Also, NAMD incorporates the distributed par allel multipole tree algorithm for full electrostatic force evaluation in O(N) time. NAMD can be connected via a communication system to a molecular graphics program in order to provide an interactive modeling tool for viewing and modifying a running simulation. The application of NAMD to a protein-water system of 32,867 atoms illus trates the performance of NAMD.
Get full access to this article
View all access options for this article.
References
1.
Abrahams, J.P., Leslie, A.G.W., Lutter, R., and Walker, J.E.1994. Structure at 2.8 angstoms resolution of F 1-ATPase from bovine heart mitochondria. Nature370:621-628.
2.
Allen, M.P., and Tildesley, D.J.1987. Computer simulation of liquids. New York: Oxford University Press.
3.
Barnes, J., and Hut, P.1986. A hierarchical θ(NlogN) force-calculation algorithm . Nature324:446-449.
4.
Berger, M.J., and Bokhari, S.H.1987. A partitioning strategy for nonuniform problems on multiprocessors . IEEE Transactions on ComputersC-36:570-580.
5.
Beveridge, D.L., and Ravishanker, G.1994. Molecular dynamics studies of DNA. Curr. Opinion Struct. Biol.4:246-255.
6.
Bishop, T., and Schulten, K.1994. Molecular dynamics study of a sequence specific protein-DNA interaction. In Computational approaches in supramolecular chemistry, edited by G. Wipff.Boston: Kluwer Academic, pp. 419-439.
7.
Bishop, T., and Schulten, K.1996. Molecular dynamics study of glucocorticoid receptor-DNA binding. Proteins: Structure, Function, andGenetics24(1):115-133.
8.
Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., and Karplus, M.1983. CHARM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem.4:187-217.
9.
Brooks, B.R., and Hodošček, M.1992. Parallelization of CHARM for MIMD machines. Chemical DesignAutomation News7:16-22.
10.
Brooks, C.L. Iii, and Karplus, M.1983. Deformable stochastic boundaries in molecular dynamics . J. Chem. Phys.79(12):6312-6325.
11.
Brooks, C.L. Iii, Karplus, M., and Pettitt, B.M.1988. Proteins: A theoretical perspective of dynamics, structure and thermodynamics. New York: John Wiley & Sons.
12.
Brünger, A.T.1992. X-PLOR, version 3.1: A system for X-ray crystallography and NMR. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University.
13.
Carson, M., and Hermans, J.1985. The molecular dynamics workshop laboratory. In Molecular dynamics and protein structure, edited by J. Hermans.Chapel Hill: University of North Carolina Press.
14.
Clark, T., Hanxleden, R., McCammon, J., and Scott, L.1994. Parallelizing molecular dynamics using spatial decomposition . In Proceedings of the Scalable High Performance Computing Conference, Knoxville, TN. Los Alamitos, CA: IEEE Computer Society Press, pp. 95-102.
15.
Deisenhofer, J., Epp, O., Mikki, K., Huber, R., and Michel, H.1985. Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3 Å resolution. Nature318:618-624.
16.
Eriksson, M., Härd, T., and Nilsson, L.1995. Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution. Biophys. J.68:402-426.
17.
Esselink, K., and Hilbers, P.1992. Parallel molecular dynamics on a torus network . In Proc. Scalable High Peformance Computing, Williamsburgh, VA. Los Alamitos, CA: IEEE Computer Society Press, pp. 106-112.
18.
Feher, G., Arno, T.R., and Okamura, M.Y.1988. The effect of an electric field on the charge recombination rate of D+QĀ → DQA in reaction centers from rhodobacter sphaeroides R-26. In The photosynthetic bacterial reaction center: Structure and dynamics, edited by J. Breton and A. Vermeglio.New York and London: Plenum , pp. 271-287.
19.
Geist, A., Beguelin, A., Dongarra, J., Jiang, W., Manchek, R., and Sunderam, V.1994. PVM 3 users guide and reference manual. Technical Manual ORNL/TM-12187. Oak Ridge National Laboratory, TN .
20.
Greengard, L., and Rokhlin, V.1987. A fast algorithm for particle simulation. J. Comp. Phys.73:325-348.
21.
Gursoy, A.1994. Simplified expression of message-driven programs and quantification of their impact on performance. Ph.D. thesis, University of Illinois at Urbana-Champaign.
22.
Haney, S.W.1994. Is C++ fast enough for scientific computing? Computers in Physics8:690-694.
23.
Harris, L.F., Sullivan, M.R., Popken-Harris, P.D., and Hickok, D.F.1994. Molecular dynamics simulations in solvent of the glucocorticoid receptor protein in complex with a glucocorticoid response element DNA sequence. J. Biom. Struct. Dyn.12:249-270.
24.
Heller, H., Schaefer, M., and Schulten, K.1993. Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal-phases. J. Phys. Chem.97:8343-8360.
25.
Iwata, S., Ostermeier, C., Ludwig, B. and Michel, H.1995. Structure at 2.8 A resolution of cytochrom C oxidase from Paracoccus denitrificans. IWAT95376:660-669.
26.
Kalé, L.V.1990. The Chare Kernel parallel programming language and system . In Proc. Int. Conf. on Parallel Processing, vol. 2, pp. 17-25. Boston: CRC Press .
27.
Kalé, L.V., and Gursoy, A.1995. Modularity, reuse and efficiency with message-driven libraries . In Proc. 7th SIAM Parallel Processing Conf, San Francisco, pp. 738-743. Philadephia : SIAM.
28.
Kalé, L.V., and Gursoy, A.1995. Modularity, reuse and efficiency with message-driven libraries . In Proceedings of the 7th SIAM.
29.
Kalé, L.V., and Krishnan, S.1993. CHARM++: A portable concurrent object-oriented system based on C++. In Proc. OOPSLA-93, Washington, DC.New York: ACM Press.
30.
Lorenz, M., Popp, D., and Holmes, K.C.1993. Refinement of the F-actin model against X-ray fiber diffraction data by the use of a directed mutation algorithm. J. Mol. Biol.234: 826-836.
31.
McCammon, J.A., and Harvey, S.C.1987. Dynamics of proteins and nucleic acids. Cambridge, UK : Cambridge University Press.
32.
Nelson, M., Humphrey, W., Gursoy, A., Dalke, A., Kalé, L., Skeel, R., Schulten, K., and Kufrin, R.1995. MDScope—A visual computing environment for structural biology. Comput. Phys. Commun.91(1-3):111-134.
33.
Pastor, R.W., and Venable, R.M.1993. Molecular and stochastic dynamics simulation of lipid molecules. In Computer simulation of biomolecular systems: Theoretical and experimental applications, edited by W. F. van Gunsteren, P. K. Weiner, and A. K. Wilkinson.Leiden : ESCOM Science Publishers, pp. 443-463.
34.
Plimpton, S., and Hendrickson, B.1994. A new parallel method for molecular dynamics simulation of macromolecular systems. Technical Report SAND94-1862. Sandia National Laboratories, NM.
35.
Rankin, W., and Board, J.A., Jr. 1995. A portable distributed implementation of the parallel multipole tree algorithm. Duke University Technical Report 95-002 . IEEE Symposium on High Performance Distributed Computing (pp. 17-22). Los Alamitos, CA: IEEE Computer Society Press.
36.
Rayment, I., Rypniewski, W.R., Schmidt-Bäse, K., Smith, R., Tomchick, D.R., Benning , M.M., Winkelmann, D.A., Wesenberg, G., and Holden, H.M.1993. Three-dimensional structure of myosin subfragment-1: A molecular motor. Science261:50-58.
37.
Schwabe, J.W.R., Chapman, L., Finch, J.T., and Rhodes, D.1993. The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: How receptors discriminate between their response elements . Cell75:567-578.
38.
Skeel, R.D., and Biesiadecki, J.J.1994. Symplectic integration with variable stepsize. AnnalsNumer. Math.1:191-198.
39.
Tirion, M.M., ben-Avraham, D., Lorenz, M., and Holmes, K.C.1995. Normal modes as refinement parameters for the F-actin model. Biophys. J.68:5-12.
40.
van Gunsteren, W.F., and Berendsen, H.J.C.1987. GROMOS manual. BIOMOS b. v., Laboratory of Physical Chemistry, University of Groningen .
41.
von Eicken, T., Culler, D.E., Goldstein, S.C., and Schauser, K.E.1992. Active messages: A mechanism for integrated communication and computation. In Proc. Int. Symp. on Computer Architecture . New York: ACM Press.
42.
Weiner, P.K., and Kollman, P.A.1981. AMBER: Assisted model building with energy refinement: A general program for modeling molecules and their interactions. J. Comp. Chem.2:287.
43.
Windemuth, A.1995. Advanced algorithms for molecular dynamics simulation: The program PMD. In Parallel computing in computational chemistry , edited by T. Mattson.Washington, DC: ACS Books.
44.
Zhou, F., and Schulten, K.1995. Molecular dynamics study of a membrane-water interface . J. Phys. Chem.99:2194-2208.
45.
Zhou, F., and Schulten, K.1996. Molecular dynamics study of the activation of phospholipase A2 on a membrane surface. Proteins: Structure, Function, and Genetics25(1):12-27.
