AMBER swMATH ID: 1333 Software Authors: D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B.P. Roberts, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossváry, K.F. Wong, F. Paesani, J. Vanicek, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko and P.A. Kollman. Description: AmberTools is a set of programs for biomolecular simulation and analysis. They are designedto work well with each other, and with the “regular” Amber suite of programs. You can performmany simulation tasks with AmberTools, and you can do more extensive simulations with thecombination of AmberTools and Amber itself. Homepage: http://ambermd.org Programming Languages: C, C++ and Fortran90 Dependencies: C, C++ and Fortran90 Keywords: molecular mechanical force fields for the simulation of biomolecules; molecular simulation programs Related Software: Gromacs; CHARMM; NAMD; CUDA; LAMMPS; APBS; VMD; Python; MIBPB; ACEMD; DESMOND; DL_POLY; OpenMM; PDB2PQR; ms2; PLUMED; HOOMD-blue; RASPA; Cassandra; Towhee Cited in: 48 Documents Standard Articles 1 Publication describing the Software, including 1 Publication in zbMATH Year AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Zbl 0886.92035Pearlman, David A.; Case, David A.; Caldwell, James W.; Ross, Wilson S.; Cheatham, Thomas E. III; DeBolt, Steve; Ferguson, David; Seibel, George; Kollman, Peter 1995 all top 5 Cited by 160 Authors 2 Anderson, Kurt S. 2 Case, David A. 2 Chen, Duan 2 Dryden, Ian L. 2 Geng, Weihua 1 Afrasiabi, M. 1 Ağacan, Ömer S. 1 Ågren, Hans 1 Ahituv, Niv 1 Akberova, N. I. 1 Alisheva, D. A. 1 Allouche, David 1 Amaro, Rommie E. 1 Anderson, Joshua A. 1 Bal, René 1 Bała, Piotr 1 Barbe, Sophie 1 Bauman, Paul T. 1 Bernaschi, Massimo 1 Beveridge, David L. 1 Bisson, Mauro 1 Biyikli, Emre 1 Board, John A. jun. 1 Burke, Kieron 1 Caldwell, James W. 1 Campagna, Giovanni 1 Carpenter, E. J. 1 Cheatham, Thomas E. III 1 Chen, Zhan 1 Cheng, Wei-Chung 1 Clancy, Thomas Charles 1 Clark, Tim W. 1 Crawford, Edward F. 1 Crozier, Paul S. 1 Cui, Qizhi 1 Czapla, Luke 1 de Givry, Simon 1 DeBolt, Steve 1 Delle Site, Luigi 1 Dixit, Surjit B. 1 Dixon, J. M. 1 El-Hassany, Ahmed 1 Engel, Michael 1 Gale, Julian D. 1 Gates, Tom S. 1 Glotzer, Sharon C. 1 Greenstein, Gil 1 Griebel, Michael 1 Gross, Eberhard K. U. 1 Grubb, Thomas L. 1 Haberl, Florian 1 Håkan, Hugosson W. 1 Harvey, Stephen C. 1 Hermans, Jan 1 Hinze, Thomas 1 Izotova, E. D. 1 Jacob, Ferosh 1 Jankowski, Eric 1 Jayaram, Balasubramaniam 1 Jensen, Frank 1 Kameoka, Shun 1 Kasheverov, I. E. 1 Kim, Kwang-Rae 1 Klein, Rupert 1 Klippel, H. 1 Kollman, Peter 1 Kueh, Kelly 1 Kulik, Marta 1 Kulkarni, Abhishek N. 1 Lanig, Harald 1 Lankhorst, Marc M. 1 Laughton, Charles A. 1 Le, Huiling 1 Leimkuhler, Benedict J. 1 Levtsova, O. V. 1 Li, Che-Wei 1 Li, Yaohang 1 Liang, Yihao 1 Lindbo, Dag 1 Liu, Tie-Fei 1 Luttighuis, Paul Oude 1 Majewski, Jacek A. 1 Mann, Geoffrey 1 Mao, Pei-Lin 1 Mardia, Kanti V. 1 Marques, Miguel A. L. 1 McConnell, K. J. 1 Melchionna, Simone 1 Mordvintsev, D. Yu. 1 Mukherjee, Rudranarayan M. 1 Narumi, Tetsu 1 Nazaruk, Mirosław 1 Newton, Ryan R. 1 Nip, M. L. A. 1 Niu, Rui-Juan 1 Nogueira, Fernando 1 Nyland, Lars 1 Odegard, Gregory M. 1 Oden, John Tinsley 1 Othersen, Olaf ...and 60 more Authors all top 5 Cited in 26 Serials 8 Journal of Computational Physics 2 Computer Methods in Applied Mechanics and Engineering 2 Computer Physics Communications 2 Molecular Simulation 2 SIAM Journal on Scientific Computing 2 Computational Biology and Chemistry 2 Communications in Computational Physics 1 International Journal of Non-Linear Mechanics 1 International Journal of Solids and Structures 1 Journal of Mathematical Physics 1 Bulletin of Mathematical Biology 1 Computer Languages 1 Mathematical and Computer Modelling 1 Signal Processing 1 Applied Mathematical Modelling 1 Cybernetics and Systems Analysis 1 Chaos 1 RAIRO. Operations Research 1 Matematicheskoe Modelirovanie 1 Multiscale Modeling & Simulation 1 Lecture Notes in Physics 1 The Annals of Applied Statistics 1 Serdica Journal of Computing 1 International Journal for Numerical Methods in Biomedical Engineering 1 Journal of Theoretical Biology 1 Wiley Series in Probability and Statistics all top 5 Cited in 17 Fields 26 Biology and other natural sciences (92-XX) 10 Statistical mechanics, structure of matter (82-XX) 9 Numerical analysis (65-XX) 9 Computer science (68-XX) 7 Quantum theory (81-XX) 6 Optics, electromagnetic theory (78-XX) 4 Mechanics of deformable solids (74-XX) 3 Statistics (62-XX) 3 Information and communication theory, circuits (94-XX) 2 Mechanics of particles and systems (70-XX) 2 Classical thermodynamics, heat transfer (80-XX) 1 General and overarching topics; collections (00-XX) 1 Combinatorics (05-XX) 1 Dynamical systems and ergodic theory (37-XX) 1 Probability theory and stochastic processes (60-XX) 1 Fluid mechanics (76-XX) 1 Operations research, mathematical programming (90-XX) Citations by Year