aa aat abc abf ABI abo Abramyan absTol Acc Accelerys Accelrys acceptor Acceptor acceptors accomx accomy accomz accuracies ach ackland Ackland acolor acos Acta actinide acylindricity addforce Addington addtorque adf Adhikari adiam adim Adjiman adof adp Adri advect advection advects affine Afshar agilio Agilio agni Agnolin Ai Aidan aij airebo Aj ajs ajaramil akohlmey Aktulga al alain Alain Alamos alat Albe alchemical AlCu Alderton Alejandre Aleksei alessandro Alessandro Alexey ali aliceblue Allinger allocaters allosws AlO Alonso alphashrink amap Amatrix AMD amino Amirjalayer Amit amu Amzallag analytical Anders Andzelm Ang anglegrad angletangrad angmom angmomx angmomy angmomz Angs anharmonic anharmonicity aniso anisotropic anisotropies anisotropy ansi antiquewhite Antisymmetrized antisymmetry anton Antonelli api Apoorva Appl Apu arallel arccos arge Archlinux arcsin arg args argv arrhenius Arun arXiv asin Askari askoose asphere ASPHERE aspherical asphericity Asq assignee assively Asta Astart Astop asub asubrama Asumming atan atc AtC ATC athermal atime atimestep athomps atm atomeye atomfile atomID atomistic attogram attograms attrac Atw Atwater atwt augt AuO automagically Avalos avalue aveforce Avendano avi AVX awpmd AWPMD Axel Axilrod Ay Ayton Az Azevedo azimuthal Azuri ba Babadi Babaei backcolor backends Baczewski Bagi Bagnold Bkappa Bal balancer Balankura Balasubramanian Balatsky Ballenegger Bammann Banna Barashev barostat Barostats barostatted barostatting Barostatting Barrat Bartels barycenter barye Bashford bashrc Baskes Batra Bayly bb bcc bcolor bdiam bdw Beckman Belak Bellott benchmarking Bennet Berardi Beraun berendsen Berendsen berger Berkowitz berlin Berne Bertotti Bessarab Beutler Bext Bfrac bgq Bh Bialke bicrystal Biersack bigbig bigint Bij bilayer bilayers binsize binstyle binutils biomolecular biomolecule Biomolecules Biophys Biosym bisectioning bispectrum Bispectrum bitbucket bitmapped bitmask bitrate bitrates Bitzek Blaise blanchedalmond blocksize blueviolet bn bni bo Bochum bocs bodyflag bodyforce bodystyle Bogaerts Bogusz Bohrs boltz Boltzman BondAngle BondBond bondchk BondingIDs bondmax bondtype Bonet Bonomi boolean boostostat boostostatting Boresch Botero Botu Bouguet Bourne boxcolor boxlo boxhi boxxlo boxxhi boxylo boxyhi boxzlo boxzhi bp bpclermont bpls br Branduardi Branicio brennan Brien Brilliantov Broadwell Broglie brownian brownw Broyden Bryantsev Btarget btype buckPlusAttr buf builtin Bulatov Bureekaew burlywood Bussi Buturigakkwaishi Buyl Bybee bz cadetblue calc calibre caltech Caltech Camilloni Camiloni Campana Cao Capolungo Caro cartesian CasP Caswell Cates cauchy cauchystat Cavazzoni Cavium Cawkwell cbecker ccache ccachepiecewise ccl ccmake ccN ccNspecies CCu cd cdeam cdennist cdof ceil Ceil centerline centro centroid Centroid centrosymmetry Cercignani cercignanilampis Cerda ceriotti Ceriotti Cerutti cfg CFG cfile CFL cgdna CGDNA cgs cgsdk CGSDK Chalopin Champaign charmm CHARMM charmmfsh charmmfsw charptr Chaudhuri checkbox checkmark checkqeq chemistries Chemnitz Cheng Chenoweth chiral ChiralIDs chiralIDs chirality Cho ChooseOffset chris Christoph Chu chunkID Ciccotti Cieplak Cii Cij cis civ CKD Clang clearstore Cleary Clebsch clemson Clermont clo Clovertown cmake CMake cmap Cmax cmd cmdlist cmds Cmin cmm CMM cn cN Cn cna cnp cnr coaxstk codebase coeff Coeff CoefficientN coeffs Coeffs cohesionless Coker Colberg coleman Colliex collinear collisional Columic colvars Colvars COLVARS comID Commun compositing compressibility compressive Comput computable compute concat cond conda Conda Condens Connor conf config configfile configurational conformational ConstMatrix Contrib cooperativity coord Coord CoordN coords coreshell cornflowerblue cornsilk corotate corotation corotational correlator cosineshifted cossq costheta Couette coul coulgauss coulombic Coulombic Coulombics Courant covalent covalently covariance cpp cpu createatoms createAtoms crespi Crespi Critchley crossterm Crowson Crozier Cryst Crystallogr Csanyi csh cshrc CSiC csld cslib CSlib cstdio cstdlib cstring cstyle csvr ctrl Ctypes ctypes cuda Cuda CUDA CuH cuFFT Cummins Curk Cusentino customIDs cutbond cuthi cutinner cutlo cutmax cutoffA cutoffC cuu cv Cv Cval cvar cvff cwiggle cygwin Cygwin cylindrically Cyrot cyrstals Daivis Dammak dampflag Darden darkblue darkcyan darkgoldenrod darkgray darkgreen darkkhaki darkmagenta darkolivegreen darkorange darkorchid darkred darksalmon darkseagreen darkslateblue darkslategray darkturquoise darkviolet Das Dasgupta dashpot dat datafile datatype datums Davidchack Daw dcd dcub Dcut de dE De decorrelation debye Debye Decius decompositions decrementing deeppink deepskyblue defgrad defn deformable del delaystep DeleteIDs deleteIDs delflag Dellago delocalization delocalized delr deltaHf Dendrimer dendritic Denniston dephase dephasing dequidt Dequidt der dereference derekt Deresiewicz Derjagin Derjaguin Derlet Deserno Destree destructor detils Devanathan devel Devemy deviatoric Devine df dfftw DFT dftb dh dhex dia diag diagonalization diagonalize diagonalized diagonalizers diagonalizing Diallo diel differentiable diffusively diffusivity dihedral dihedrals Dihedrals dihydride Dij dimdim dimensioned dimensionality dimgray dipolar dir Direc dirname discoverable discretization discretized disp dissipative Dissipative distharm dl dlambda DLAMMPS dll dlopen dm dmax Dmax dmg dmi dnf DNi Dobson Dodds docenv dodgerblue dof doi Donadio dotc Doty doxygen doxygenclass doxygenfunction downarrow Doye dpd DPD dpdTheta dphi DPhil dr dR dragforce Drautz dreiding Dreiding drfourth drho drsquared drude Drude DRUDE dsf dsmc dt dtgrow dtheta dtshrink du dU Dudarev Duin Dullweber dumpfile Dunbrack Dunweg Dupont dUs dV dvector dVx dW dx dy dylib dyn dyne dynes dynmat Dyre Dzyaloshinskii Eaa Eaat Eacn eam eangle earg eatom Eb Eba Ebeling ebend ebond ebook ebt ec Ec eco ecoul ecp Ecut EdgeIDs edgeIDs edihed edim edip edn edpd eDPD edu ee Eebt ees eFF efield effm eflux eg Eggebrecht ehex eHEX Ei eigen eigensolve eigensolver eigensolvers eigendecomposition eigenvalue eigenvalues eigenvector eigenvectors eij Eij Eijnden Eike eim eimp Eindhoven Eisenforschung Ejtehadi El elaplong Electroneg electronegative electronegativity Eleftheriou ElementN elementset elementsets elif Elj Ellad ellipsoidflag elong Elsevier Elsner Elstner elt emacs emax Emax Embt emi emol eN energetics energyCorr eng Engility engilitycorp engrot engtrans engvib enobonds EnSight enthalpy enums envoke eos epair epcc epl Epp Epq eps Epton epub ePUB eq eqal eqch Eqp Eqq Eqs equi equil equilibrate equilibrated equilibrates equilibrating equilibration Equilibria equilization Ercolessi Erdmann eradius erate erc erf erfc Erhart erorate erose erotate errno Ertas ervel Espanol Eshelby eshelby eskm esph estretch esu esub esw et etag etap ETarget ethernet etol etot etotal etube Eulerian eulerian eulerimplicit Europhys ev eV evalue Evanseck evdwl evector evec evecs eval evals Everaers Evgeny evirials ewald Ewald excitations excv exe executables extep extrema exy ey ez faceset facesets factorizable factorizations Fahrenberger Faken Farago Fasolino Fath Fava fbMC Fc fcc fcm Fd fd fdotr fdt Fehlberg Fellinger fe femtosecond femtoseconds fene Fennell fep FEP fermi Fermionic Ferrand fexternal Fexternal ffield ffl ffmpeg FFmpeg ffplay fft fftbench fftw fgets fhg Fi Fichthorn Fickian fieldname figshare Fij filelink filename Filename filenames Filenames Fily fileper filesystem Fincham Finchham Finnis Fiorin fixID fj Fji flagfld flagHI flaglog flagN flagVF fld floralwhite Florez flv fmackay fmag fmass fmm fmt fmx fmy fmz fN Fn fname fno Fnudge foces Fock Fogarty Foiles fopenmp forceclear forestgreen formatarg formulae Forschungszentrum Fortran fortran Fosado fourier fp fphi fPIC fplo Fqq Fraige framerate Frauenheim Fraunhofer fread Freitas Frenkel Friedrichs fs fsh fstyle fsw ftm ftol fugacity Fumi func funcs functionalities functionals funroll fuer fx fy fz Gahler gainsboro Galindo gamA gammaA gammaFactor gammaR gamR Gan GaN ganzenmueller Ganzenmuller Gao Gathert Gaus gauss gaussian gaussians Gaussians Gavhane gayberne gcc gcmc gdot GeC Geier gencode georg Georg Germann Germano gerolf Gerolf Gershgorin gettimeofday gewald Gezelter Gflop gfortran ghostwhite Giacomo gif gifsicle Gillan Gingold Gissinger github gjf gjwagne gl gladky Gladky gld gle globbing Glosli Glotzer gmail gmake gmask Gmask gneb GNEB Goldfarb Gonzalez-Melchor googlemail Gordan GPa gpu gpuID gpus gradgradflag gradV GradVidottan graining Graining Grama grana granregion graphene Greathouse greenyellow Greffet grem gREM Grest Grigera Grimme grmask Grmask gromacs Gromacs gromos Gronbech Groot groupbig groupbit grp Grueneisen gsmooth gstyle GTL Gubbins Guericke Guenole gui Gumbsch Gunsteren Gunzenmuller Guo gw gyromagnetic gz gzipped Haak Hafskjold halfstepback Halperin Halver Hamaker Hamel haptic Hara Harpertown Harting Hartree Hartrees Hasan Hashtable Haswell Haugk Hayoun Hayre hbar hbcut hbn hbnewflag hbond hcp heatconduction Hebenstreit Hecht Heenen Hendrik Henin Henkelman Henkes henrich Henrich Hermitian Herrmann Hertizian hertzian Hertzsch hexahedrons hexatic hexorder Heyes HfO hgrid hhmrr Hibbs Higdon Hijazi Hilger histo histogrammed histogramming hma hmaktulga hplanck hoc Hochbruck Hofling Holian Holm holonomic Homebrew hooke Hookean hotpink Houlle howto Howto Hoyt Hs hstyle html hTST https hu Hueckel Huetter Hugonio hugoniostat Hugoniostat Hugoniot Hura hux hwloc hx hy hydrophobicity hydrostatic hydrostatically Hynninen Hyoungki hyperdynamics hyperplane hyperradius hyperspherical hysteretic hz Ibanez iatom ibar ibm icc ico icosahedral idealgas IDR idx ie ielement ieni ifdefs iff ifort Ihle ij ijk ijkl ik Ikeshoji ilmenau Ilmenau ilp Ilya im Im imageint Imageint Imagemagick imd Impey impl impropers Impropers imulator includelink incompressible incrementing indenter indenters indianred indices inertiax inertiay inertiaz infile infty inhomogeneities inhomogeneous init initialdelay initializations initio InP inregion instantiation Institut integrators Integrators intel intelmpi interal interatomic Interatomic interconvert interial interlayer intermolecular Interparticle interstitials intertube Intr intra intralayer intramolecular ints inv invariants inversed ionocovalent iostreams iparam ipi ipp Ippolito IPv IPython ipython Isele isenthalpic ish Ishida iso isodemic isoenergetic isoenthalpic isokinetic isomorphism isothermal isotropically isovolume Isralewitz iter iters iteratively Ith Itsets itype itypeN iva Ivanov Ivector Iw iwyu ixcm ixx Ixx ixy Ixy ixz Ixz iy iycm iyy Iyy iyz Iyz iz izcm ized Izrailev Izumi Izvekov izz Izz Jacobsen Jadhav jagreat Jalalvand james Janssen Janssens Jaramillo Jarzynski jatempl javascript jcp jea jec Jeffers jewett Jewett ji Jiang Jiao jik JIK jku jN Joannopoulos Jochim Jonsson Jorgensen jp jparam jpeg jpeglib jpg JPG jpl Jth jtranch jtype jtypeN Juelich Julien junghans Junghans Jungnickel Jupyter Justo Jusufi Jx Jy Jz jzimmer Kadiri Kai Kalia Kamberaj Kapfer Karls Karlsruhe Karniadakis Karplus Karttunen kate Katsnelson Katsura Kaufmann Kawata Kaxiras Kayser kb kB kbit kbits kcal kcl Kd KDevelop ke KE Keblinski Keefe keflag Keir Kelchner Kelkar Kemper kepler keV Keyes Khersonskii Khrapak Khvostov Ki Kikugawa kim kinetostats kJ kk Klahn Klapp Kloss Kloza kmax Kmax KMP kmu Knizhnik knl Kofke kofke Kohlmeyer Kohn kokkos Kolafa Kollman kolmogorov Kolmogorov Kondor konglt Koning Kooser Korn Koskinen Koster Kosztin Kp Kraker Kraus Kremer Kress Kronik ksh kspace Kspace KSpace Kspring kT kTequil kth Kth kTln ktypeN Kub Kubo Kumagai Kumar Kurebayashi Kuronen Kusters Kutta Kuznetsov kx Lackmann Ladd lagrangian lambdai lamda LambdaLanczos lammps Lammps LAMMPS lammpsplot Lampis Lamoureux Lanczos Lande Landron langevin Langevin Langston lanl larentzos Larentzos Laroche lars latencies Latour latourr lattce Laupretre Lauriat lavenderblush lawngreen lB lbfgs lbl LBtype lcbop ld ldfftw ldg lebedeva Lebedeva Lebold Lechman Lehoucq Leimkuhler Leite leiu lemonchiffon Lenart lennard Lennard Lenosky Lenz Lett Leuven Leven Lewy lgvdw Liang libatc libAtoms libawpmd libch libcolvars libcurl libdir libdl libfftw libgcc libgpu libjpeg libkim liblammps Liblammps liblink libmeam libmessage libmpi libmpich libnuma libplumed libplumedKernel libpng libpoems libqmmm librar libreax libs Lifshitz ligand lightblue lightcoral lightcyan lightgoldenrodyellow lightgreen lightgrey lightpink lightsalmon lightseagreen lightskyblue lightslategray lightsteelblue lightyellow Likhtman limegreen linalg Lindahl lineflag lineforce linesearch linux Liouville Lisal listfile Littmark Liu Livermore lj llammps LLVM lm lmp lmpptr lmpqst lmpsdata Lmpsdata lmptype LMT ln localTemp localvectors Loewen logfile logfreq logicals Lomdahl Lond lookup lookups Lookups LoopVar Lorant lorenz Los lossless lossy Lozovik lps lpsapi lrt lsfftw ltbbmalloc lubricateU lucy Luding Lussetti Lustig lval lwsock lx ly Lybrand Lyulin lz Maaravi Mackay Mackrodt Macromolecules macroparticle MacOS Madura Magda Magdeburg magelec Maginn magneton magnetons mainboard mainboards makefile Makefile makefiles Makefiles makelist makepkg Makse malloc Malolepsza Manby Mandadapu Mandelli Manh manifoldforce Manolopoulos manpages manybody MANYBODY Maras Marchetti Marchi Mariella Marinica Marrink Marroquin Marsaglia Marseille Martyna mary marys Masaglia Mashayak Massimilliano massless masstotal Masuhiro Matchett Materias mathbf mathjax matlab matplotlib Matsubara Mattice Mattox Mattson maxangle maxbond maxchunk maxelt maxeval maxfiles Maxfoo maxima maxit maxiter maxsize maxspecial maxSteps maxstrain maxwell Maxwellian maxX Mayergoyz Mayoral mbt Mbytes MBytes mc McLachlan md mdf mdpd mDPD meam meamc MEAMC meamf meanDist mech Mecke mediumaquamarine mediumblue mediumorchid mediumpurple mediumseagreen mediumslateblue mediumspringgreen mediumturquoise mediumvioletred Mees Mehl Mei Melchor Meloni Melrose Mem mem memalign MEMALIGN membered memcheck Mendelev mer Meremianin Mersenne Merz meshless meso mesocnt MESODPD mesodpd MESONT mesont mesoparticle mesoscale mesoscopic metadata metadynamics Metadynamics Methfessel methine Metin meV Mezei mgpt MGPT mgptfast mh micelle micelles michael michele Mickel microcanonical microelastic microporous Microscale midnightblue mie Mie Mij Mikami Militzer Minary mincap Mindlin minhbonds mingw minima minimizations minimizer minimizers minneigh minorder minSteps mintcream Mintmire Miron mis Mises Mishin Mishra mistyped mistyrose Mj mK mkdir mkv mliap mlparks Mniszewski mnt mobi modc Modell modelled modelling Modelling Modine mofff MOFFF Mohd Mohles mol Mol molfile Molfile moltemplate momb Monaghan Monaghans monodisperse monodispersity monovalent Montalenti Montero Morefoo Morfill Mori Moriya morris Morriss morse Morteza Mosayebi Moseler Moskalev Moustafa mov mpi MPI mpicc mpiCC mpich mpicolor mpicxx mpiexec mpiio mpirun mplayer mps Mryglod mscg MSCG msd msi MSI msm msse msst Mtchell Mth mtk Mtotal muB Muccioli mui Mukherjee Mulders mult multi multibody Multibody multicenter multicmd multicomponent multicore multielectron multinode multiphysics multiscale multisectioning multithreading Multithreading Mundy Murdick Murtola Murty Muser Muto muVT mux muy muz mv mV Mvapich mvh mvv MxN myCompute myIndex mylammps MyPool mysocket myTemp myVec na nabla Nagaosa Nakano nall namespace namespaces namedtuple nan NaN Nandor nangles Nangletype nangletypes Nangletypes nano nanoindentation Nanoletters nanomechanics nanometer nanometers nanoparticles Nanotube nanotube nanotubes Narulkar nasa nasr natively Natoli natoms Natoms Nattempt navajowhite Navier nb Nbin Nbins nbody Nbody nbonds nbondtype Nbondtype nbondtypes Nbondtypes nBOt nbrhood Nbtypes nc Nc nchunk Nchunk ncoeff ncol ncorr ncount nd ndihedrals Ndihedraltype Ndirango ndof Ndof Ndouble ndx neb neel Neel Neelov Negre nelem nelems Nelement Nelements nemd netcdf netstat Nettleton Neumann Nevent nevery Nevery newfile Newns newtype Neyts Nf nfft nfile Nfile Nfreq ng Ng nghost Nghost Ngpu Ngyuen nh nharmonic nhc nhi NiAlH Nicklas Niklasson Nikolskiy nimpropers Nimpropertype Ninteger Nissila nist nitride nitrides niu Nk nktv nl nlen Nlines nlo nlocal Nlocal Nlog nlp nm Nm Nmax nmax Nmin nmin Nmols nn Nocedal nocite nocoeff nodeless nodeset nodesets Noehring Noffset noforce Noid nolib nonequilibrium nongauss nonGaussian nonlocal Nonlocal Noordhoek nopreliminary Nord norder Nordlund normals Noskov noslip noticable noutcol Noutput noutrow Novik Novint np Npair Npairs nparams nparticle npernode nph NpH Nphi nphug nprocs Nprocs npt nr Nr Nrecompute Nrepeat nreset Nrho Nroff nrow nrun Ns Nsample Nskip Nspecies ns nsq Nstart nstats Nstep Nsteplast Nstop nsub Nswap Nt Ntable ntheta nthreads ntimestep Ntptask Ntriples Ntype ntypes Ntypes nucleotides num numa numactl numdiff numericalfreedom numerics numpy Numpy Nurdin Nvalue Nvaluelast Nvalues nvc nvcc nve nvidia nvk nvt Nwait nwchem nx Nx nxnodes ny Ny nz Nz ocl octahedral octants Ohara ohenrich ok Okabe Okamoto O'Keefe OKeefe oldlace olecular Oleinik Olfason olivedrab Ollila omegaDD omegax omegay omegaz Omelyan omp OMP onelevel oneway onn ons OO opencl openKIM openmp OpenMP openmpi opls Oppelstrup optimizations orangered organometallic orientational orientationsFile orientorder Orlikowski ornl Ornstein Orsi ortho orthonormal orthorhombic oso ot Otype Ouldridge outfile outmost outputss Ouyang overdamped overlayed Ovito oxdna oxrna oxDNA oxRNA packings padua Padua pafi palegoldenrod palegreen paleturquoise palevioletred Panagiotopoulos Pandit Papaconstantopoulos papayawhip paquay Paquay parallelepiped Parallelizable parallelization parallelized parallelizing param parameterization parameterizations parameterize parameterized params ParaView parmin Parrinello Partay Particuology pastewka Pastewka pathangle pathname pathnames Patomtrans Pattnaik Pavese Pavia Paxton pbc pc pchain Pchain Pdamp pdb pdf pdfs pdim pe Peachey peachpuff Pearlman Pedersen peID PEigenDense Peng peptide peratom Pergamon peri peridynamic Peridynamic peridynamics Peridynamics perl permittivity perp Perram persp Persp peru Peskin Pettifor pfactor pgi ph Philipp Phillpot Philos phiphi phonon phonons phophorous phosphide Phs Physica physik Piaggi picocoulomb picocoulombs picogram picograms picosecond picoseconds pid piecewise Pieniazek Pieter pimd Piola Pisarev Pishevar Pitera pj pjintve planeforce Plathe Plimpton plog ploop PloS plt plumedfile pmb Pmolrotate Pmoltrans pN png Podhorszki Poiseuille poisson Polak polarizabilities polarizability polarizable Polarizable polarizables polarizer Politano polyA polybond polydisperse polydispersity polyelectrolyte polyhedra polymorphism popen Popov popstore Poresag pos Poschel posix Postma Potapkin potin Pourtois powderblue ppn pppm prd Prakash pre Pre prec precession prefactor prefactors prepend prepended preprint printf printflag priori Priya proc Proc procs Prony progguide ps Ps pscreen pscrozi pseudodynamics pseudopotential Pstart Pstop pstyle Ptarget pthread pthreads ptm PTM ptol ptr pu purdue Purohit pushstore pvar pw pwqmmm px Px pxx Pxx Pxy py Py pydir pylammps PyLammps pymbar pymodule pymol pypar pythonic Pyy pz Pz Pzz qbmsst qcore qdist qE qe qeff qelectron qeq QeQ QEq qfactor qfile qi Qi qj Qj Ql qm Qmin qmmm qmol qoffload qopenmp qoverride qqr qqrd qtb quadratically quadrupolar Quant quartic quat quaternion quaternions quati quatj quatk quatw queryargs Queteschiner qw qx qy qz radian radians Rafferty rahman Rahman Raman ramped ramping Ramprasad Randisi randomizations Raphson Rappe Ravelo rc Rc Rcm rcmax Rcmx Rcmy Rcut rcutfac rdc rdf RDideal rdx reacter realTypeMap real_t README realtime reamin reax REAXC ReaxFF rebo recursing Ree refactored refactoring reflectionstyle regoin Reinders reinit relaxbox relink relTol remappings remd Ren Rendon reneighbor reneighboring Reneighboring reneighborings Rensselaer reparameterizing repo representable Reproducibility reproducibility repuls rescale rescaled rescales rescaling Rescaling respa RESPA respecified responder resquared REsquared restartfile restartinfo rethrowing Revenga rewrap rezwanur rfac rfile rg Rg Rhaphson rheological rheology rhodo Rhodo rhodopsin rhok rhorho rhosum ri Ri Ribiere richard rigidID rigidify rij rIJ Rij RIj Rik Rin Rino RiRj Risi Rix Riy rj Rj Rjinner RjinnerN Rjk rjones Rjouter RjouterN rk rkf Rkinner RkinnerN Rkouter RkouterN rmask Rmask rmass rmax Rmax rmdir rmin Rmin RMS rmsd rnage rNEMD ro Rochus Rockett Rodrigues Rohart Ronchetti Ronevich Rosati Rosenberger Rossky rosybrown rotationally Rovigatti royalblue rozero Rperp Rr rRESPA Rspace rsq rst rstyle Rubensson Rubia Rudd Rudra Rudranarayan Rudzinski Runge runtime Rutuparna rx ry rz Ryckaert Rycroft Rydbergs Rz Sabry saddlebrown Sadigh saed safezone Safran Sagui Saidi Salles sandia Sandia sandybrown sanitizer Sanyal sc scafacos SCAFACOS scalability scalable Scalable scalexy scalexz scaleyz Schaik Schilfgarde Schimansky Schiotz Schlitter Schmid Schratt Schoen 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Tchain Tcom tcsh tdamp tdpd tDPD Tdrude Technol Telsa tempCorrCoeff templated Templeton Tequil ters tersoff Tersoff tesselation Tetot tex tfac tfmc tfMC th Thakkar Thaokar thb thei Theodorou Theor thermalization thermalize thermalized Thermalized thermalizing Thermalizing thermo thermochemical thermochemistry thermodynamically Thermophysical thermostatted thermostatting Thermostatting Thes Thess Thexe Thiaville Thibaudeau Thijsse Thirumalai threebody thrid ThunderX thylakoid THz Tigran Tij Tildesley timespan timestamp timestamps timestep timestepping timesteps TiN TiO Tirrell Titer Tji Tk Tkin tloop tlsph tmax Tmax tmd tmin Tmin tmp tN Tobias Tohoku tokenizer tokyo tol tomic toolchain topologies Toporov Torder torsions Tosi Toukmaji Toxvaerd tpa tpc tpm tptask tqx tqy tqz traceless tradeoff traj Tranchida transactional transferability translational Translational trate Tref Tretyakov tri triangleflag Tribello triclinic Triclinic triflag trigonal trilinear Trinkle tripflag tris trj trott 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