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Found 201 Software Packages (Results 1–100)

Gromacs

Software Authors:   Mark James Abraham; Teemu Murtola; Roland Schulz; Szilárd Páll; Jeremy C.Smith; Berk Hess; Erik Lindahl
Referenced in: 99 Publications (2002–2022)
Related Software: NAMD; CHARMM; LINCS; AMBER; VMD; LAMMPS; …
Main Fields: Numerical analysis (65-XX); Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX)

APBS

Software Authors:   Nathan Baker; J. Andrew McCammon; Michael Holst
Referenced in: 91 Publications (2001–2022)
Related Software: MIBPB; CHARMM; TABI; PDB2PQR; PBEQ-Solver; SG; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Optics, electromagnetic theory (78-XX)

VMD

Software Authors:   Andrew Dalke, William Humphrey, Klaus Schulten
Referenced in: 75 Publications (1999–2023)
Related Software: NAMD; Gromacs; CHARMM; PyMOL; RasMol; APBS; …
Main Fields: Numerical analysis (65-XX); Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX)

NAMD

Software Authors:   James Phillips
Referenced in: 64 Publications (1999–2019)
Related Software: Gromacs; CHARMM; VMD; AMBER; CUDA; LAMMPS; …
Main Fields: Numerical analysis (65-XX); Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX)

LAMMPS

Software Authors:   Plimpton, Steve
Referenced in: 60 Publications (1995–2022)
Related Software: Gromacs; Python; NAMD; Peridigm; CUDA; CHARMM; …
Main Fields: Numerical analysis (65-XX); Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX)

BioNetGen

Software Authors:   Michael L. Blinov; James R. Faeder; Byron Goldstein; William S. Hlavacek
Referenced in: 55 Publications (2008–2022)
Related Software: Bio-PEPA; NFsim; COPASI; PySB; BIOCHAM; LBS; …
Main Fields: Ordinary differential equations (34-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)

ABINIT

Software Authors:   Xavier Gonze; et al.
Referenced in: 47 Publications (2004–2022)
Related Software: Quantum Espresso; CASTEP; CheFSI; NWChem; lobpcg.m; WIEN2k; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Mechanics of deformable solids (74-XX)

NWChem

Software Authors:   Kendall, Ricky A.; Aprà, Edoardo; Bernholdt, David E.; Bylaska, Eric J.; Dupuis, Michel; Fann, George I.; Harrison, Robert J.; Ju, Jialin; Nichols, Jeffrey A.; Nieplocha, Jarek; Straatsma, T.P.; Windus, Theresa L.; Wong, Adrian T.
Referenced in: 40 Publications (2000–2022)
Related Software: GAUSSIAN; ABINIT; LAPACK; Quantum Espresso; GAMESS; ScaLAPACK; …
Main Fields: Numerical analysis (65-XX); Computer science (68-XX); Quantum theory (81-XX)

PDB2PQR

Software Authors:   T. Dolinsky, J. Nielsen, A. McCammon, N. Baker
Referenced in: 33 Publications (2006–2022)
Related Software: APBS; MIBPB; TABI; CHARMM; PBEQ-Solver; DelPhi; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Optics, electromagnetic theory (78-XX)

DL_POLY

Software Authors:   Smith, W.; Yong, C.W.; Rodger, P.M.
Referenced in: 24 Publications (2000–2020)
Related Software: Gromacs; CHARMM; DL_POLY_3; AMBER; DL_MONTE; MDAnalysis; …
Main Fields: Numerical analysis (65-XX); Mechanics of deformable solids (74-XX); Quantum theory (81-XX)

PERMIX

Software Authors:   Talebi, Hossein; Silani, Mohammad; Bordas, Stéphane P.A.; Kerfriden, Pierre; Rabczuk, Timon
Referenced in: 24 Publications (2014–2022)
Related Software: XFEM; CutFEM; FEniCS; Matlab; ABAQUS; hypre; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Computer science (68-XX)

SIESTA

Software Authors:   Soler J.S., Artacho E., Gale J.D., Garcia A., Junquera J., Ordejon P., Sanchez-Portal D
Referenced in: 22 Publications (2006–2022)
Related Software: ONETEP; CASTEP; ABINIT; OCTOPUS; CONQUEST; ScaLAPACK; …
Main Fields: Numerical analysis (65-XX); Computer science (68-XX); Mechanics of deformable solids (74-XX)

VAMPnets

Software Authors:   Andreas Mardt, Luca Pasquali, Hao Wu, Frank Noé
Referenced in: 22 Publications (2019–2022)
Related Software: PDE-Net; torchdiffeq; TensorFlow; SINDy; GAIO; PRMLT; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Operator theory (47-XX); Numerical analysis (65-XX)

LIGGGHTS

Software Authors:   Kloss, C., Goniva, C.
Referenced in: 20 Publications (2014–2022)
Related Software: OpenFOAM; CFDEMcoupling; Mathematica; MFIX-DEM; LAMMPS; STAR-CCM+; …
Main Fields: Numerical analysis (65-XX); Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX)

NAMD2

Software Authors:   Kale, Laxmikant; Skeel, Robert; Bhandarkar, Milind; Brunner, Robert; Gursoy, Attila; Krawetz, Neal; Phillips, James; Shinozaki, Aritomo; Varadarajan, Krishnan; Schulten, Klaus
Referenced in: 17 Publications (1998–2016)
Related Software: CHARMM; Gromacs; VMD; NAMD; AMBER; Globus Toolkit; …
Main Fields: Numerical analysis (65-XX); Computer science (68-XX); Mechanics of deformable solids (74-XX)

GULP

Software Authors:   Gale, Julian D.; Rohl, Andrew L.
Referenced in: 19 Publications (1986–2017)
Related Software: Open Babel; VASP; XtalOpt; Avogadro; ReaxFF; SIESTA; …
Main Fields: Mathematical logic and foundations (03-XX); Computer science (68-XX); Mechanics of deformable solids (74-XX)

PARSEC

Software Authors:   J.R. Chelikowsky
Referenced in: 20 Publications (2008–2020)
Related Software: ARPACK; lobpcg.m; CheFSI; ABINIT; FEAST; LAPACK; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Mechanics of deformable solids (74-XX)

ASE

Software Authors:   Hjorth Larsen, A.; Jørgen Mortensen, J.; Blomqvist, J.; Castelli, I. E.; Christensen, R.; Dułak, M.; Friis, J.; Groves, M. N.; Hammer, B.; Hargus, C.; Hermes, E. D.; Jennings, P. C.; Bjerre Jensen, P.; Kermode, J.; Kitchin, J. R.; Leonhard Kolsbjerg, E.; 14 Kubal, J.; Kaasbjerg, K.; Lysgaard, S.; Bergmann Maronsson, J.; Maxson, T.; Olsen, T.; Pastewka, L.; Peterson, A.; Rostgaard, C.; Schiøtz, J.; Schütt, O.; Strange, M.; Thygesen, K.; Vegge, T.; Vilhelmsen, L.; Walter, M.; Zeng, Z.; Jacobsen, K. W
Referenced in: 3 Publications (2019–2022)
Related Software: Python; pymatgen; NumPy; SciPy; Spglib; Atomate; …
Main Fields: Probability theory and stochastic processes (60-XX); Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX)

ESPResSo

Software Authors:   Limbach, H.-J.; Arnold, A.; Mann, B. A.; Holm, C
Referenced in: 14 Publications (2008–2021)
Related Software: NAMD; Gromacs; ESPResSo++; AdResS; MMM2D; Python; …
Main Fields: Numerical analysis (65-XX); Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX)

UNICORE

Software Authors:   Huber, Valentina
Referenced in: 13 Publications (2001–2010)
Related Software: NorduGrid; Globus Toolkit; GridSim; GridLab; EMan; ASKALON; …
Main Fields: Numerical analysis (65-XX); Computer science (68-XX); Game theory, economics, finance, and other social and behavioral sciences (91-XX)

VASP

Software Authors:   Jürgen Hafner; Georg Kresse; Doris Vogtenhuber; Martijn Marsman
Referenced in: 8 Publications (2004–2018)
Related Software: Quantum Espresso; Spglib; Python; GAUSSIAN; WIEN2k; Open Babel; …
Main Fields: Numerical analysis (65-XX); Computer science (68-XX); Mechanics of deformable solids (74-XX)

GSHMC

Software Authors:   Akhmatskaya, Elena; Reich, Sebastian
Referenced in: 16 Publications (2008–2020)
Related Software: Gromacs; NUTS; PyMC; Stan; CODA; UCI-ml; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Numerical analysis (65-XX)

MUPHY

Software Authors:   Bernaschi, M.; Melchionna, S.; Succi, S.; Fyta, M.; Kaxiras, E.; Sircar, J. K.
Referenced in: 16 Publications (2010–2019)
Related Software: Hemelb; waLBerla; Palabos; MUSCLE 2; DistMesh; likwid; …
Main Fields: Numerical analysis (65-XX); Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX)

STAPL

Software Authors:   An, Ping; Jula, Alin; Rus, Silvius; Saunders, Steven; Smith, Tim; Tanase, Gabriel; Thomas, Nathan; Amato, Nancy; Rauchwerger, Lawrence
Referenced in: 12 Publications (1992–2021)
Related Software: Boost; STL; PBGL; BGL; Boost C++ Libraries; Chapel; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

Packmol

Software Authors:   Martínez, L., Andrade, R., Birgin, E.G., Martínez, J.M.
Referenced in: 13 Publications (2012–2022)
Related Software: ALGENCAN; SPG; nanoHUB; nusimm; Polymatic; Mdtraj; …
Main Fields: Combinatorics (05-XX); Convex and discrete geometry (52-XX); Mechanics of deformable solids (74-XX)

PLUMP

Software Authors:   Beg, Ivan; Ling, Wu; M\"uller, Andreas; Przybyszewski, Piotr; R\"uhl, Roland; Sawyer, William
Referenced in: 14 Publications (1991–2009)
Related Software: PROGRES; SPARSKIT; ITSOL
Main Fields: Algebraic geometry (14-XX); Category theory; homological algebra (18-XX); Real functions (26-XX)

CPMD

Software Authors:   CPMD is jointly copyrighted by IBM Corporation and Max-Planck Institut, Stuttgart.
Referenced in: 12 Publications (1999–2012)
Related Software: AMBER; ACEMD; DESMOND; Gromacs; NAMD; Sequoia Benchmark; …
Main Fields: Numerical analysis (65-XX); Computer science (68-XX); Optics, electromagnetic theory (78-XX)

DESMOND

Software Authors:   D. E. Shaw Research
Referenced in: 7 Publications (2010–2018)
Related Software: Gromacs; NAMD; LAMMPS; AMBER; CHARMM; CUDA; …
Main Fields: Numerical analysis (65-XX); Statistical mechanics, structure of matter (82-XX); Biology and other natural sciences (92-XX)

HyperChem

Software Authors:   Howard A., McIver J., Collins J; Hypercube, Inc.
Referenced in: 13 Publications (2006–2018)
Related Software: GAP; GAUSSIAN; Fullerene; FuiGui; Magma; DRAGON; …
Main Fields: Combinatorics (05-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)

SETTLE

Software Authors:   S. Miyamoto; P. A. Kollman
Referenced in: 12 Publications (1997–2019)
Related Software: LINCS; Gromacs; NAMD; PRMLT; Chaospy; APBS; …
Main Fields: Numerical analysis (65-XX); Fluid mechanics (76-XX); Quantum theory (81-XX)

DYANA

Software Authors:   Güntert, Peter; Wüthrich, Kurt
Referenced in: 11 Publications (2001–2020)
Related Software: CYANA; CNS; word2vec; LSQR; TINKER; CPLEX; …
Main Fields: Linear and multilinear algebra; matrix theory (15-XX); Geometry (51-XX); Computer science (68-XX)

TINKER

Software Authors:   Washington University School of Medicine; Ponder, J., et al
Referenced in: 9 Publications (2002–2019)
Related Software: NDL; VTDIRECT95; PaGMO/PyGMO; CHARMM; Gromacs; AMBER; …
Main Fields: Numerical analysis (65-XX); Mechanics of deformable solids (74-XX); Statistical mechanics, structure of matter (82-XX)

WIGGLE

Software Authors:   Lee, Sang-Ho; Palmo, Kim; Krimm, Samuel
Referenced in: 10 Publications (2005–2017)
Related Software: LAMMPS; CUDA; Bolsig; FEAPpv; SETTLE; LINCS
Main Fields: Probability theory and stochastic processes (60-XX); Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX)

MDAnalysis

Software Authors:   Gowers, R. J.; Linke, M.; Barnoud, J.; Reddy, T. J.E.; Melo, M. N.; Seyler, S. L.
Referenced in: 1 Publication (2018)
Related Software: Python; NumPy; Gromacs; OpenMM; HOOMD-blue; SciPy; …
Main Fields: Fluid mechanics (76-XX)

Pi4U

Software Authors:   Hadjidoukas, P.E.; Angelikopoulos, P.; Papadimitriou, C.; Koumoutsakos, P.
Referenced in: 9 Publications (2015–2022)
Related Software: CMA-ES; ABC-SubSim; TORC; PSUADE; QUESO; DAKOTA; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

POMULT

Software Authors:   S.C. Farantos
Referenced in: 8 Publications (1998–2021)
Related Software: AUTO; Python; UPOsHam; RODES; Lorenz-Database; ADIFOR; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-XX); Mechanics of particles and systems (70-XX)

SchNet

Software Authors:   Schütt, K.; Kindermans, P-J; Felix, H. E S.; Chmiela, S.; Tkatchenko, A.; Müller, K-R
Referenced in: 8 Publications (2019–2022)
Related Software: Adam; SchNetPack; JAX; GitHub; TensorFlow; VENUS96; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Computer science (68-XX)

CP2K

Software Authors:   https://sourceforge.net/p/cp2k/_members/; Hutter J., Iannuzzi M., Schiffmann F., VandeVondele J.
Referenced in: 4 Publications (2016–2020)
Related Software: Quantum Espresso; AdResS; TensorFlow; GAUSSIAN; ASE; Python; …
Main Fields: Probability theory and stochastic processes (60-XX); Numerical analysis (65-XX); Mechanics of deformable solids (74-XX)

ProtoMol

Software Authors:   Matthey, Thierry; Cickovski, Trevor; Hampton, Scott; Ko, Alice; Ma, Qun; Nyerges, Matthew; Raeder, Troy; Slabach, Thomas; Izaguirre, Jesús A.
Referenced in: 8 Publications (2003–2015)
Related Software: OOMPAA; GSHMC; NAMD2; Gromacs; MPI; BALL; …
Main Fields: Numerical analysis (65-XX); Fluid mechanics (76-XX); Quantum theory (81-XX)

Qbox

Software Authors:   F.Gygi
Referenced in: 5 Publications (2010–2019)
Related Software: Quantum Espresso; NWChem; Python; lobpcg.m; ELPA; ABINIT; …
Main Fields: Linear and multilinear algebra; matrix theory (15-XX); Numerical analysis (65-XX); Quantum theory (81-XX)

UHBD

Software Authors:   J. Madura, J. Briggs, R. Wade, M. Davis, B. Luty, A. Ilin, J. Antosiewicz, M. Gilson, B. Bagheri, L. Scott, J. McCammon
Referenced in: 8 Publications (1999–2019)
Related Software: APBS; MIBPB; TABI; PBEQ-Solver; TMSmesh; PDB2PQR; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Computer science (68-XX)

WavePacket

Software Authors:   Burkhard Schmidt, Ulf Lorenz, Carsten Hartmann
Referenced in: 4 Publications (2009–2020)
Related Software: QuTiP; Matlab; QEngine; MCTDH; Nevergrad; NLopt; …
Main Fields: Partial differential equations (35-XX); Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-XX)

ACEMD

Software Authors:   Harvey M., Giupponi G., De Fabritiis G.
Referenced in: 3 Publications (2011–2016)
Related Software: CUDA; NAMD; AMBER; CHARMM; Gromacs; MUPHY; …
Main Fields: Numerical analysis (65-XX); Fluid mechanics (76-XX); Statistical mechanics, structure of matter (82-XX)

IMD

Software Authors:   Jörg Stadler, Erik Bitzek, Peter Brommer, Franz Gähler, Christopher Kohler, Frank Pister, Johannes Roth, Steffen Sonntag
Referenced in: 6 Publications (2000–2016)
Related Software: ACEMD; OpenMM; PuReMD; CHARMM; LAMMPS; Gromacs; …
Main Fields: Numerical analysis (65-XX); Mechanics of deformable solids (74-XX); Quantum theory (81-XX)

yt

Software Authors:   Matthew J. Turk, Britton D. Smith, Jeffrey S. Oishi, Stephen Skory, Samuel W. Skillman, Tom Abel, Michael L. Norman
Referenced in: 3 Publications (2016–2017)
Related Software: NumPy; Python; Matplotlib; h5py; unyt; SciPy; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Fluid mechanics (76-XX)

DL_POLY_3

Software Authors:   Todorov, I.T.; Smith, W.
Referenced in: 5 Publications (2004–2020)
Related Software: DL_POLY; DL_MONTE; NumPy; SciPy; Jupyter; MDAnalysis; …
Main Fields: Numerical analysis (65-XX); Mechanics of deformable solids (74-XX); Optics, electromagnetic theory (78-XX)

DynamO

Software Authors:   M. N. Bannerman, R. Sargant, L. Lue
Referenced in: 5 Publications (2015–2021)
Related Software: CHARMM; AMBER; DESMOND; NAMD; Gromacs; LAMMPS
Main Fields: Numerical analysis (65-XX); Mechanics of particles and systems (70-XX); Mechanics of deformable solids (74-XX)

REACH

Software Authors:   Kei Moritsugua, Jeremy C. Smith
Referenced in: 6 Publications (1997–2009)
Related Software:
Main Fields: Mathematical logic and foundations (03-XX); Statistics (62-XX); Computer science (68-XX)

sPuReMD

Software Authors:   Aktulga, Hasan Metin; Pandit, Sagar A.; Van Duin, Adri C.T.; Grama, Ananth Y.
Referenced in: 5 Publications (2012–2020)
Related Software: ReaxFF; PuReMD; CUDA; NAMD; LAMMPS; Gromacs; …
Main Fields: Numerical analysis (65-XX); Computer science (68-XX); Mechanics of deformable solids (74-XX)

Moldy

Software Authors:   K. Refson
Referenced in: 5 Publications (2000–2010)
Related Software: LPMD; DL_POLY_3
Main Fields: Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX); Quantum theory (81-XX)

PLUMED

Software Authors:   Massimiliano Bonomi, Davide Branduardi, Giovanni Bussi, Carlo Camilloni, Davide Provasi, Paolo Raiteri, Davide Donadio, Fabrizio Marinelli, Fabio Pietrucci, Ricardo A. Broglia, Michele Parrinello
Referenced in: 1 Publication (2017)
Related Software: Gromacs; NAMD; AMBER; VMD; OpenMM; DESMOND; …
Main Fields: Fluid mechanics (76-XX); Biology and other natural sciences (92-XX)

TREMOLO-X

Software Authors:   M. Griebel; J. Hamaekers; Fraunhofer SCAI
Referenced in: 4 Publications (2004–2017)
Related Software: Python; Atomistix ToolKit; ATK-Classical; GDAL; FastDTW; ms2; …
Main Fields: General and overarching topics; collections (00-XX); Numerical analysis (65-XX); Mechanics of deformable solids (74-XX)

AUTO_DERIV

Software Authors:   S. Stamatiadis, R. Prosmiti, S.C. Farantos
Referenced in: 4 Publications (2000–2010)
Related Software: ADIFOR; ADOL-C; POMULT; Cosy; TaylUR; HSL; …
Main Fields: Numerical analysis (65-XX); Computer science (68-XX)

Bio3d

Software Authors:   Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
Referenced in: 2 Publications (2014–2021)
Related Software: RaptorX-Angle; GeoPCA; clusfind; conformalInference; k-means++; BAMBI; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

BioPhysConnectoR

Software Authors:   Hoffgaard, F.; Weil, P.; Hamacher, K.
Referenced in: 2 Publications (2010)
Related Software: R; VMD; Pfam; Python; RHmm; BLAST; …
Main Fields: Probability theory and stochastic processes (60-XX); Biology and other natural sciences (92-XX); Systems theory; control (93-XX)

MarDyn

Software Authors:   C. Niethammer, M. Buchholz, M. Bernreuther, M. Horsch, W. Eckhardt, H. Hasse, H.-J. Bungartz, J. Vrabec
Referenced in: 4 Publications (2014–2021)
Related Software: HE-E1GODF; FEAP; LB3D; Peano; waLBerla
Main Fields: Numerical analysis (65-XX); Fluid mechanics (76-XX)

PEACH

Software Authors:   Komeiji, Yuto; Inadomi, Yuichi; Nakano, Tatsuya
Referenced in: 4 Publications (2004–2006)
Related Software: ABINIT-MP; GAMESS; AutoDock; TRANSFAC; KEGG; DOCK
Main Fields: Computer science (68-XX); Quantum theory (81-XX); Statistical mechanics, structure of matter (82-XX)

PLMLA

Software Authors:   Shi, S. P.; Qiu, J. D.; Sun, X. Y.
Referenced in: 4 Publications (2012–2019)
Related Software: Cd-hit; iSNO-PseAAC; EnsemblePail; iHyd-PseAAC; iNitro-Tyr; Cell-PLoc; …
Main Fields: Biology and other natural sciences (92-XX)

ReaDDy

Software Authors:   Johannes Schöneberg, Frank Noé
Referenced in: 3 Publications (2016–2018)
Related Software: STEPS; URDME; MesoRD; na14; Gmsh; CGAL; …
Main Fields: Partial differential equations (35-XX); Probability theory and stochastic processes (60-XX); Numerical analysis (65-XX)

ABINIT-MP

Software Authors:   Komeiji, Yuto; Inadomi, Yuichi; Nakano, Tatsuya
Referenced in: 3 Publications (2004–2005)
Related Software: PEACH; GAMESS; AutoDock; TRANSFAC; KEGG; DOCK
Main Fields: Computer science (68-XX); Quantum theory (81-XX); Biology and other natural sciences (92-XX)

COOL

Software Authors:   Paolo Barletta
Referenced in: 3 Publications (1998–2011)
Related Software: BECOOL; COBRA; PGAPack
Main Fields: Computer science (68-XX); Fluid mechanics (76-XX); Quantum theory (81-XX)

DeePMD-kit

Software Authors:   Han Wang, Linfeng Zhang, Jiequn Han, Weinan E
Referenced in: 1 Publication (2021)
Related Software: TensorFlow; Adam; Slurm; dpdata; AiiDA; GAUSSIAN; …
Main Fields: Numerical analysis (65-XX); Mechanics of deformable solids (74-XX); Statistical mechanics, structure of matter (82-XX)

DP-GEN

Software Authors:   Yuzhi Zhang, Haidi Wang, Weijie Chen, Jinzhe Zeng, Linfeng Zhang, Han Wang, Weinan E
Referenced in: 1 Publication (2022)
Related Software: Slurm; TensorFlow; dpdata; AiiDA; GAUSSIAN; LAMMPS; …
Main Fields: Probability theory and stochastic processes (60-XX); Numerical analysis (65-XX)

M.DynaMix

Software Authors:   Alexander P. Lyubartsev, Aatto Laaksonen
Referenced in: 3 Publications (2000–2010)
Related Software: VMD
Main Fields: Fluid mechanics (76-XX); Quantum theory (81-XX); Statistical mechanics, structure of matter (82-XX)

MACI

Software Authors:   Krause, Dorian; Fackeldey, Konstantin; Krause, Rolf
Referenced in: 3 Publications (2014–2022)
Related Software: Trilinos; PETSc; ParMoonolith; DOLFIN; MpCCI; PUMA; …
Main Fields: Numerical analysis (65-XX); Computer science (68-XX); Fluid mechanics (76-XX)

MDBenchmarks

Software Authors:   Favata, A; Micheletti, A; Ryu, S; Pugno, NM
Referenced in: 3 Publications (2016–2018)
Related Software: Mathematica
Main Fields: Mechanics of deformable solids (74-XX); Statistical mechanics, structure of matter (82-XX)

Mdtraj

Software Authors:   R.T. McGibbon, K.A. Beauchamp, M.P. Harrigan, C. Klein, J.M. Swails, C.X. Hernández, C.R. Schwantes, L.P. Wang, T.J. Lane, V.S. Pande
Referenced in: 0 Publications
Related Software: Python; VMD; OpenMM; Gromacs; PyMOL; ESPResSo++; …
Main Fields:

MolAxis

Software Authors:   Eitan Yaffe, Dan Fishelovitch, Haim J. Wolfson, Dan Halperin, Ruth Nussinov
Referenced in: 1 Publication (2010)
Related Software: Powercrust; Spherical Code; 3D Alpha Shapes; Mathematica; CGAL
Main Fields: Combinatorics (05-XX); Convex and discrete geometry (52-XX); Numerical analysis (65-XX)

MOLE

Software Authors:   Petřek, M., Košinová, P., Koča, J., Otyepka, M.
Referenced in: 3 Publications (2013–2018)
Related Software: VirtualGL; Open Inventor; VizServer; MeVisLab; N4itk; dcm4che; …
Main Fields: General and overarching topics; collections (00-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

Paje

Software Authors:   Chassin de Kergommeaux, J.; Stein, B.; Bernard, P.E.
Referenced in: 2 Publications (2000–2009)
Related Software: PARAVER; SIMGRID; Jumpshot; VAMPIR; KOJAK; NAS Parallel Benchmarks; …
Main Fields: Computer science (68-XX)

PuReMD

Software Authors:   Kylasa, S.B.; Aktulga, H.M.; Grama, A.Y.
Referenced in: 3 Publications (2014–2020)
Related Software: ReaxFF; sPuReMD; LAMMPS; CUDA; ILUT; ACEMD; …
Main Fields: Numerical analysis (65-XX); Statistical mechanics, structure of matter (82-XX)

Pwpaw

Software Authors:   Tackett, A. R.; Holzwarth, N. A. W.; Matthews, G. E.
Referenced in: 3 Publications (2001–2019)
Related Software: AtomPAW; Quantum Espresso; ABINIT; PAW; lobpcg.m; JASMIN; …
Main Fields: Special functions (33-XX); Computer science (68-XX); Quantum theory (81-XX)

PyEMMA

Software Authors:   Scherer, M. K.; Trendelkamp-Schroer, B.; Paul, F.; Pérez-Hernández, G.; Hoffmann, M.; Plattner, N.; Wehmeyer, C.; Prinz, J.-H.; Noé, F.
Referenced in: 2 Publications (2020–2021)
Related Software: cesium; Banpei; ta; TA-Lib; surfboard; SigPy; …
Main Fields: Linear and multilinear algebra; matrix theory (15-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

Qmd-plot

Software Authors:   Kalat, S., Mann, G., Hermans, J.
Referenced in: 2 Publications (2002–2011)
Related Software: TRAJELIX; Eucb; NAMD; NAMD2; CHARMM; Gromacs; …
Main Fields: Numerical analysis (65-XX); Statistical mechanics, structure of matter (82-XX); Biology and other natural sciences (92-XX)

QUB

Software Authors:   Nicolai, C.
Referenced in: 3 Publications (2016–2018)
Related Software: DRAGON; Penn Treebank; Tiburon; OpenFst
Main Fields: Partial differential equations (35-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)

Quickstep

Software Authors:   J. VandeVondele, M. Krack, F. Mohamed, M. Parrinello, T. Chassaing, J. Hutter
Referenced in: 1 Publication (2018)
Related Software: NWChem; ABINIT; GAUSSIAN; GPAW; HONPAS; SelInv; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Statistical mechanics, structure of matter (82-XX)

RLSCODE

Software Authors:   Stankovic, Igor; Kröger, Martin; Hess, Siegfried
Referenced in: 3 Publications (2002–2003)
Related Software:
Main Fields: Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX); Statistical mechanics, structure of matter (82-XX)

S/PHI/nX

Software Authors:   S. Boeck, C. Freysoldt, A. Dick, L. Ismer, J. Neugebauer
Referenced in: 2 Publications (2010–2019)
Related Software: PAW; Pwpaw; AtomPAW; lobpcg.m; JASMIN; Quantum Espresso; …
Main Fields: Special functions (33-XX); Computer science (68-XX); Quantum theory (81-XX)

SediFoam

Software Authors:   Rui Sun, Heng Xiao
Referenced in: 3 Publications (2018–2021)
Related Software: FLUENT
Main Fields: Fluid mechanics (76-XX); Geophysics (86-XX)

SELM

Software Authors:   Wang, Y.; Sigurdsson, J.K.; Atzberger, P.J.
Referenced in: 3 Publications (2016–2019)
Related Software: Surface Evolver; SymPy; Jython; LAMMPS
Main Fields: Partial differential equations (35-XX); Global analysis, analysis on manifolds (58-XX); Numerical analysis (65-XX)

Simbody

Software Authors:   Seth, Ajay; Sherman, Michael; Eastman, Peter; Delp, Scott
Referenced in: 2 Publications (2010–2015)
Related Software: OpenSim; Puppeteer; Simox; RBDL; Matlab; Octave; …
Main Fields: Mechanics of particles and systems (70-XX); Biology and other natural sciences (92-XX)

Aboria

Software Authors:   M. Robinson, M. Bruna
Referenced in: 2 Publications (2017–2019)
Related Software: FEniCS; Gmsh; Matlab
Main Fields: Partial differential equations (35-XX); Probability theory and stochastic processes (60-XX); Fluid mechanics (76-XX)

ACPYPE

Software Authors:   A. da Silva, W. Vranken
Referenced in: 2 Publications (2012–2014)
Related Software: Gromacs; ZIBMolPy; ZIBgridfree; Chimera; GANM; GROMOS; …
Main Fields: Biology and other natural sciences (92-XX); Information and communication theory, circuits (94-XX)

Bill2d

Software Authors:   Solanpää, J.; Luukko, P.J.J.; Räsänen, E.
Referenced in: 1 Publication (2016)
Related Software: Julia; Dynamicalbilliards.jl
Main Fields: Dynamical systems and ergodic theory (37-XX); Mechanics of particles and systems (70-XX)

CHARMM-GUI

Software Authors:   Jo, S., Kim, T., Iyer, V.G., et al.
Referenced in: 1 Publication (2017)
Related Software: P-LINCS; OpenMM; VMD; LINCS; PLUMED; Gromacs
Main Fields: Fluid mechanics (76-XX); Biology and other natural sciences (92-XX)

Cormorant

Software Authors:   Brandon Anderson, Truong-Son Hy, Risi Kondor
Referenced in: 2 Publications (2020–2022)
Related Software: mad-GP; MULTIMODE; PhysNet; SchNet; JAX; DScribe; …
Main Fields: Probability theory and stochastic processes (60-XX); Game theory, economics, finance, and other social and behavioral sciences (91-XX); Biology and other natural sciences (92-XX)

CPPTRAJ

Software Authors:   Roe, D. R.; Cheatham, T. E.
Referenced in: 1 Publication (2019)
Related Software: PyTraj; cookiecutter; pdb-tools; VMD; OpenMM; PLUMED; …
Main Fields: Biology and other natural sciences (92-XX)

Dalton

Software Authors:   Aidas, K.; Angeli, C.; Bak, K. L.; Bakken, V.; Bast, R.; Boman, L.; Christiansen, O.; et al.
Referenced in: 1 Publication (2020)
Related Software: SPHINX; EinSum; CuPy; Jmol; Psi4NumPy; NumPy; …
Main Fields: Statistical mechanics, structure of matter (82-XX)

i-pi

Software Authors:   Michele Ceriotti, Joshua More, David E. Manolopoulos
Referenced in: 1 Publication (2018)
Related Software: Adam; Gromacs; Torch; Caffe; TensorFlow; DeePMD-kit; …
Main Fields: Computer science (68-XX); Quantum theory (81-XX); Biology and other natural sciences (92-XX)

Ibisco

Software Authors:   Karimi-Varzaneh, H. A.; Qian, H. J.; Chen, X.; Carbone, P.; Müller-Plathe, F.
Referenced in: 1 Publication (2013)
Related Software:
Main Fields: Mechanics of deformable solids (74-XX)

iMembrane

Software Authors:   S. Kelm, J. Shi, C.M. Deane
Referenced in: 1 Publication (2014)
Related Software: UniProt; WebGestalt; KDDONTO; Protege; GeoSVM; GAMES; …
Main Fields: General and overarching topics; collections (00-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

lobSTR

Software Authors:   Melissa Gymrek; David Golan; Saharon Rosset; Yaniv Erlich
Referenced in: 1 Publication (2016)
Related Software: PPS; Matlab
Main Fields: Harmonic analysis on Euclidean spaces (42-XX); Biology and other natural sciences (92-XX)

MateriApps LIVE

Software Authors:   Yuichi Motoyama; Kazuyoshi Yoshimi; Takeo Kato; Synge Todo
Referenced in: 0 Publications
Related Software: mVMC; CONQUEST; DCore; DSQSS; GAMESS; hphi; …
Main Fields:

McVol

Software Authors:   Till, M., Ullmann, G.
Referenced in: 2 Publications (2011–2020)
Related Software: Voronoia; CGAL; SBL; MolSurfComp; GitHub; Voro++; …
Main Fields: Convex and discrete geometry (52-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

MDStressLab

Software Authors:   Chandra Admal, Nikhil; Tadmor, Ellad B.
Referenced in: 2 Publications (2010–2016)
Related Software:
Main Fields: Mechanics of deformable solids (74-XX)

MDVRY

Software Authors:   M. Souaille, H. Loirat, D. Borgis, M.P. Gaigeot
Referenced in: 2 Publications (2009–2013)
Related Software: MCMC2; GROMOS
Main Fields: Numerical analysis (65-XX); Fluid mechanics (76-XX); Optics, electromagnetic theory (78-XX)

MesoBioNano

Software Authors:   I. A. Solov'yov, A. V. Yakubovich, P. V. Nikolaev, I. Volkovets, A. V. Solov'yov
Referenced in: 2 Publications (2013–2022)
Related Software: LOQUAT; BCM; Mathematica
Main Fields: Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX); Statistical mechanics, structure of matter (82-XX)

MOIL

Software Authors:   Elber, R.; Roitberg, A.; Simmerling, C.; Goldstein, R.; Li, H.; Verkhivker, G.; Keasar, C.; Zhang, J.; Ulitsky, A.
Referenced in: 2 Publications (1999–2005)
Related Software: NAMD2; STL; MPI; OOMPAA
Main Fields: Computer science (68-XX); Statistical mechanics, structure of matter (82-XX)

ms2

Software Authors:   S. Deublein, B. Eckl, J. Stoll, et al.
Referenced in: 1 Publication (2017)
Related Software: AMBER; VMD; Cassandra; RASPA; FEASST; Etomica; …
Main Fields: General and overarching topics; collections (00-XX); Numerical analysis (65-XX)

MSMBuilder

Software Authors:   Harrigan, MP; Sultan, MM; Hernandez, CX; Husic, BE; Eastman, P; Schwantes, CR; Beauchamp, KA; McGibbon, RT; Pande, VS
Referenced in: 1 Publication (2018)
Related Software: GPy; Python; Scikit; Osprey; NNDB; MODENA; …
Main Fields: Probability theory and stochastic processes (60-XX); Numerical analysis (65-XX); Computer science (68-XX)