VMD swMATH ID: 18651 Software Authors: Dalke, Andrew; Humphrey, William; Schulten, Klaus Description: VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. Homepage: http://www.ks.uiuc.edu/Research/vmd/ Related Software: Gromacs; NAMD; CHARMM; PyMOL; RasMol; APBS; Chimera; PDB2PQR; Python; OpenMM; CUDA; Jmol; AMBER; R; TABI; LAMMPS; Quantum Espresso; Wannier90; Open Babel; OVITO Cited in: 79 Documents all top 5 Cited by 256 Authors 3 Chen, Zhen 3 Lin, Lin 3 Shen, Luming 2 Damle, Anil 2 Geng, Weihua 2 Ilieva, Nevena 2 Jiang, Xi Zhuo 2 Kalé, Laxmikant V. 2 Karniadakis, George Em 2 Konieczny, Leszek 2 Luo, Kai Hong 2 Roterman, Irena 2 Schulten, Klaus 2 Skeel, Robert D. 2 Tozzini, Valentina 1 Amaro, Rommie E. 1 Amat, Pietro 1 An, Dong 1 Andriukaitis, Darius 1 Arnold, Axel 1 Asghari, Mohsen 1 Atwal, Harpreet K. 1 Ayub, Nicolás 1 B. R., Abhiram 1 Banach, Mateusz 1 Barba, Lorena A. 1 Barclay, Paul L. 1 Bardhan, Jaydeep P. 1 Bauman, Paul T. 1 Beni, Yaghoub Tadi 1 Benros, Cristina 1 Berini, Carolina 1 Bhandarkar, Milind 1 Bian, Xin 1 Birgin, Ernesto G. 1 Board, John A. jun. 1 Bonaccorso, Fabio 1 Bonella, Sara 1 Botello Rionda, Salvador 1 Boutilier, Michael S. H. 1 Brunger, Axel T. 1 Brunner, Robert J. 1 Brylinski, Michal 1 Bu, Bing 1 Buehler, Markus J. 1 Buttry, Daniel A. 1 Camiola, Vito Dario 1 Carbone, Alessandra 1 Carrillo-Tripp, Mauricio 1 Chen, Jiahui 1 Chen, Xiaole 1 Chen, Yiran 1 Chen, Zhiguo 1 Chiodo, Letizia 1 Coveney, Peter V. 1 Cruz-Chú, Eduardo R. 1 Czapla, Luke 1 de Brevern, Alexandre G. 1 De Fabritiis, Gianni 1 Delp, Scott L. 1 Demkowicz, Leszek 1 Deng, Mingge 1 Diao, Jiajie 1 Dib, Linda 1 Ding, Yanhong 1 Durve, Mihir 1 Eargle, John 1 Eastman, Peter 1 Eslahchi, Changiz 1 Fahrenberger, Florian 1 Fath, L. 1 Feng, Muye 1 Filippi, Simonetta 1 Fu, Yi 1 Gao, David Yang 1 Gao, Huajian 1 Ghosh, Debraj 1 Gogolinska, Anna 1 Greiner, Walter 1 Grinberg, Leopold 1 Gu, Yuantong 1 Gupta, Munish Kumar 1 Gursoy, Attila 1 Habibi, Mahnaz 1 Hagen, Hans-Juergen 1 Hamacher, Kay 1 Hamada, Tsuyoshi 1 Hamann, Bernd 1 Han, Huiyun 1 Hao, Xuejun 1 Harvey, M. J. 1 Hazout, Serge 1 He, Jiadi 1 Hege, Hans-Christian 1 Heider, Yousef 1 Hermans, Jan 1 Hernandez Padilla, Carlos Alberto 1 Hernandez, Alan E. Lopez 1 Herrera-Guzmán, Rafael 1 Hochbruck, Marlis ...and 156 more Authors all top 5 Cited in 36 Serials 11 Journal of Computational Physics 5 Computer Physics Communications 5 Computational Biology and Chemistry 4 Computer Methods in Applied Mechanics and Engineering 4 Acta Mechanica Sinica 4 Communications in Computational Physics 4 Journal of Theoretical Biology 3 Journal of Mathematical Chemistry 3 Computational & Mathematical Methods in Medicine 2 Computers and Fluids 2 Journal of the Mechanics and Physics of Solids 2 RAIRO. Operations Research 2 Multiscale Modeling & Simulation 2 Algorithms 1 Acta Mechanica 1 Computers & Mathematics with Applications 1 International Journal of Solids and Structures 1 Journal of Statistical Physics 1 Mathematics and Computers in Simulation 1 Theoretical Computer Science 1 Computer Aided Geometric Design 1 Computers & Operations Research 1 Computational Mechanics 1 SIAM Journal on Scientific Computing 1 Engineering Analysis with Boundary Elements 1 Nonlinear Dynamics 1 European Journal of Mechanics. A. Solids 1 European Journal of Mechanics. B. Fluids 1 Discrete and Continuous Dynamical Systems. Series B 1 International Journal of Computational Methods 1 International Journal of Numerical Analysis and Modeling 1 International Journal of Structural Stability and Dynamics 1 Molecular Based Mathematical Biology 1 Proceedings of the Royal Society of London. A. Mathematical, Physical and Engineering Sciences 1 Mathematics and Visualization 1 Computational and Mathematical Biophysics all top 5 Cited in 19 Fields 45 Biology and other natural sciences (92-XX) 18 Mechanics of deformable solids (74-XX) 17 Numerical analysis (65-XX) 16 Statistical mechanics, structure of matter (82-XX) 12 Fluid mechanics (76-XX) 5 Computer science (68-XX) 4 Optics, electromagnetic theory (78-XX) 3 Partial differential equations (35-XX) 3 Quantum theory (81-XX) 2 Statistics (62-XX) 2 Operations research, mathematical programming (90-XX) 2 Information and communication theory, circuits (94-XX) 1 General and overarching topics; collections (00-XX) 1 Algebraic geometry (14-XX) 1 Linear and multilinear algebra; matrix theory (15-XX) 1 Integral equations (45-XX) 1 Differential geometry (53-XX) 1 Global analysis, analysis on manifolds (58-XX) 1 Systems theory; control (93-XX) Citations by Year