| Year |
Citation |
Score |
| 2017 |
Skeel RD, Zhao R, Post CB. A minimization principle for transition paths of maximum flux for collective variables. Theoretical Chemistry Accounts. 136. PMID 29225509 DOI: 10.1007/S00214-016-2041-3 |
0.339 |
|
| 2017 |
Skeel R, Fang Y. Comparing Markov Chain Samplers for Molecular Simulation Entropy. 19: 561. DOI: 10.3390/E19100561 |
0.395 |
|
| 2016 |
Hardy DJ, Wolff MA, Xia J, Schulten K, Skeel RD. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations. The Journal of Chemical Physics. 144: 114112. PMID 27004867 DOI: 10.1063/1.4943868 |
0.434 |
|
| 2016 |
Skeel RD. An alternative construction of the Ewald sum Molecular Physics. 114: 3166-3170. DOI: 10.1080/00268976.2016.1222455 |
0.359 |
|
| 2015 |
Hardy DJ, Wu Z, Phillips JC, Stone JE, Skeel RD, Schulten K. Multilevel Summation Method for Electrostatic Force Evaluation. Journal of Chemical Theory and Computation. 11: 766-779. PMID 25691833 DOI: 10.1021/Ct5009075 |
0.371 |
|
| 2014 |
Fang Y, Sanz-Serna JM, Skeel RD. Compressible generalized hybrid Monte Carlo. The Journal of Chemical Physics. 140: 174108. PMID 24811626 DOI: 10.1063/1.4874000 |
0.41 |
|
| 2011 |
Skeel RD, Reich S. Corrected potential energy functions for constrained molecular dynamics European Physical Journal: Special Topics. 200: 55-72. DOI: 10.1140/Epjst/E2011-01518-8 |
0.404 |
|
| 2010 |
Zhao R, Shen J, Skeel RD. Maximum Flux Transition Paths of Conformational Change. Journal of Chemical Theory and Computation. 6: 2411-2423. PMID 20890401 DOI: 10.1021/Ct900689M |
0.342 |
|
| 2009 |
Hairer E, McLachlan RI, Skeel RD. ON ENERGY CONSERVATION OF THE SIMPLIFIED TAKAHASHI-IMADA METHOD. Esaim. Mathematical Modelling and Numerical Analysis = Esaim. Modelisation Mathematique Et Analyse Numerique : M=2an. 43: 631-644. PMID 20539750 DOI: 10.1051/M2An/2009019 |
0.404 |
|
| 2009 |
Skeel RD. WHAT MAKES MOLECULAR DYNAMICS WORK? Siam Journal On Scientific Computing : a Publication of the Society For Industrial and Applied Mathematics. 31: 1363-1378. PMID 20084278 DOI: 10.1137/070683660 |
0.415 |
|
| 2009 |
Sweet CR, Hampton SS, Skeel RD, Izaguirre JA. A separable shadow Hamiltonian hybrid Monte Carlo method. The Journal of Chemical Physics. 131: 174106. PMID 19894997 DOI: 10.1063/1.3253687 |
0.426 |
|
| 2007 |
Skeel RD, Hardy DJ, Phillips JC. Correcting Mesh-Based Force Calculations to Conserve Both Energy and Momentum in Molecular Dynamics Simulations. Journal of Computational Physics. 225: 1-5. PMID 18591998 DOI: 10.1016/J.Jcp.2007.03.010 |
0.367 |
|
| 2005 |
Wang W, Skeel RD. Fast evaluation of polarizable forces. The Journal of Chemical Physics. 123: 164107. PMID 16268681 DOI: 10.1063/1.2056544 |
0.401 |
|
| 2005 |
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry. 26: 1781-802. PMID 16222654 DOI: 10.1002/Jcc.20289 |
0.382 |
|
| 2005 |
Engle RD, Skeel RD, Drees M. Monitoring energy drift with shadow Hamiltonians Journal of Computational Physics. 206: 432-452. DOI: 10.1016/J.Jcp.2004.12.009 |
0.404 |
|
| 2004 |
Zou G, Skeel RD. Robust variance reduction for random walk methods Siam Journal On Scientific Computing. 25: 1964-1981. DOI: 10.1137/S1064827503424025 |
0.562 |
|
| 2003 |
Zou G, Skeel RD. Robust biased Brownian dynamics for rate constant calculation. Biophysical Journal. 85: 2147-57. PMID 14507681 DOI: 10.1016/S0006-3495(03)74641-4 |
0.54 |
|
| 2003 |
Ma Q, Izaguirre JA, Skeel RD. Verlet-I/r-RESPA/Impulse is limited by nonlinear instabilities Siam Journal On Scientific Computing. 24: 1951-1973. DOI: 10.1137/S1064827501399833 |
0.367 |
|
| 2003 |
Wang W, Skeel RD. Analysis of a few numerical integration methods for the Langevin equation Molecular Physics. 101: 2149-2156. DOI: 10.1080/0026897031000135825 |
0.38 |
|
| 2002 |
Skeel RD, Tezcan I, Hardy DJ. Multiple grid methods for classical molecular dynamics. Journal of Computational Chemistry. 23: 673-84. PMID 11939600 DOI: 10.1002/Jcc.10072 |
0.413 |
|
| 2002 |
Skeel RD, Hardy DJ. Practical construction of modified Hamiltonians Siam Journal On Scientific Computing. 23: 1172-1188. DOI: 10.1137/S106482750138318X |
0.392 |
|
| 2002 |
Skeel RD, Izaguirre JA. An impulse integrator for Langevin dynamics Molecular Physics. 100: 3885-3891. DOI: 10.1080/0026897021000018321 |
0.395 |
|
| 2001 |
Skeel RD, Srinivas K. Nonlinear stability analysis of area-preserving integrators Siam Journal On Numerical Analysis. 38: 129-148. DOI: 10.1137/S0036142998349527 |
0.315 |
|
| 2001 |
Lzaguirre JA, Catarello DP, Wozniak JM, Skeel RD. Langevin stabilization of molecular dynamics Journal of Chemical Physics. 114: 2090-2098. DOI: 10.1063/1.1332996 |
0.374 |
|
| 2000 |
Zou G, Skeel RD, Subramaniam S. Biased Brownian dynamics for rate constant calculation. Biophysical Journal. 79: 638-45. PMID 10919998 DOI: 10.1016/S0006-3495(00)76322-3 |
0.512 |
|
| 1999 |
Izaguirre JA, Reich S, Skeel RD. Longer time steps for molecular dynamics Journal of Chemical Physics. 110: 9853-9864. DOI: 10.1063/1.478995 |
0.325 |
|
| 1999 |
Skeel RD. Symplectic integration with floating-point arithmetic and other approximations Applied Numerical Mathematics. 29: 3-18. DOI: 10.1016/S0168-9274(98)00033-6 |
0.377 |
|
| 1999 |
Hardy DJ, Okunbor DI, Skeel RD. Symplectic variable step size integration for N-body problems Applied Numerical Mathematics. 29: 19-30. DOI: 10.1016/S0168-9274(98)00031-2 |
0.376 |
|
| 1999 |
Kalé L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K. NAMD2: Greater Scalability for Parallel Molecular Dynamics Journal of Computational Physics. 151: 283-312. DOI: 10.1006/Jcph.1999.6201 |
0.342 |
|
| 1999 |
Schlick T, Skeel RD, Brunger AT, Kalé LV, Board JA, Hermans J, Schulten K. Algorithmic Challenges in Computational Molecular Biophysics Journal of Computational Physics. 151: 9-48. DOI: 10.1006/Jcph.1998.6182 |
0.323 |
|
| 1998 |
Garcia-Archilla B, Sanz-Serna JM, Skeel RD. Long-time-step methods for oscillatory differential equations Siam Journal On Scientific Computing. 20: 930-963. DOI: 10.1137/S1064827596313851 |
0.399 |
|
| 1998 |
Schlick T, Mandziuk M, Skeel RD, Srinivas K. Nonlinear Resonance Artifacts in Molecular Dynamics Simulations Journal of Computational Physics. 140: 1-29. DOI: 10.1006/Jcph.1998.5879 |
0.381 |
|
| 1997 |
López-Marcos MA, Sanz-Serna JM, Skeel RD. Explicit symplectic integrators using Hessian-vector products Siam Journal On Scientific Computing. 18: 223-238. DOI: 10.1137/S1064827595288085 |
0.413 |
|
| 1997 |
Skeel RD, Zhang G, Schlick T. A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications Siam Journal On Scientific Computing. 18: 203-222. DOI: 10.1137/S1064827595282350 |
0.413 |
|
| 1997 |
Littell TR, Skeel RD, Zhang M. Error analysis of symplectic multiple time stepping Siam Journal On Numerical Analysis. 34: 1792-1807. DOI: 10.1137/S0036142995287094 |
0.436 |
|
| 1997 |
Zhang M, Skeel RD. Cheap implicit symplectic integrators Applied Numerical Mathematics. 25: 297-302. DOI: 10.1016/S0168-9274(97)00066-4 |
0.384 |
|
| 1997 |
Bishop TC, Skeel RD, Schulten K. Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics Journal of Computational Chemistry. 18: 1785-1791. DOI: 10.1002/(Sici)1096-987X(19971115)18:14<1785::Aid-Jcc7>3.0.Co;2-G |
0.36 |
|
| 1995 |
Barth E, Kuczera K, Leimkuhler B, Skeel RD. Algorithms for constrained molecular dynamics Journal of Computational Chemistry. 16: 1192-1209. DOI: 10.1002/Jcc.540161003 |
0.433 |
|
| 1995 |
Zhang M, Skeel RD. Symplectic integrators and the conservation of angular momentum Journal of Computational Chemistry. 16: 365-369. DOI: 10.1002/Jcc.540160309 |
0.349 |
|
| 1994 |
Okunbor DI, Skeel RD. Canonical Runge-Kutta-Nyström methods of orders five and six Journal of Computational and Applied Mathematics. 51: 375-382. DOI: 10.1016/0377-0427(92)00119-T |
0.347 |
|
| 1994 |
Okunbor DI, Skeel RD. Canonical numerical methods for molecular dynamics simulations Journal of Computational Chemistry. 15: 72-79. DOI: 10.1002/Jcc.540150109 |
0.441 |
|
| 1993 |
Tam H, Skeel RD. Stability of Parallel Explicit ODE Methods Siam Journal On Numerical Analysis. 30: 1179-1192. DOI: 10.1137/0730061 |
0.356 |
|
| 1993 |
Skeel RD. Variable step size destabilizes the Störmer/leapfrog/verlet method Bit. 33: 172-175. DOI: 10.1007/Bf01990352 |
0.328 |
|
| 1993 |
Biesiadecki JJ, Skeel RD. Dangers of Multiple Time Step Methods Journal of Computational Physics. 109: 318-328. DOI: 10.1006/Jcph.1993.1220 |
0.447 |
|
| 1992 |
Okunbor D, Skeel RD. An Explicit Runge–Kutta–Nyström Method is Canonical If and Only If Its Adjoint is Explicit Siam Journal On Numerical Analysis. 29: 521-527. DOI: 10.1137/0729032 |
0.409 |
|
| 1992 |
Okunbor D, Skeel RD. Explicit canonical methods for hamiltonian systems Mathematics of Computation. 59: 439-455. DOI: 10.1090/S0025-5718-1992-1136225-3 |
0.361 |
|
| 1992 |
Guo R, Skeel RD. An algebraic hierarchical basis preconditioner Applied Numerical Mathematics. 9: 21-32. DOI: 10.1016/0168-9274(92)90064-K |
0.343 |
|
| 1992 |
Skeel RD, Gear CW. Does variable step size ruin a symplectic integrator? Physica D: Nonlinear Phenomena. 60: 311-313. DOI: 10.1016/0167-2789(92)90247-K |
0.337 |
|
| 1992 |
Skeel RD, Tam HW. Limits of parallelism in explicit ODE methods Numerical Algorithms. 2: 337-349. DOI: 10.1007/Bf02139473 |
0.41 |
|
| 1991 |
Skeel RD. Macromolecular dynamics on a shared-memory multiprocessor Journal of Computational Chemistry. 12: 175-179. DOI: 10.1002/Jcc.540120206 |
0.362 |
|
| 1990 |
Skeel RD, Berzins M. A Method for the Spatial Discretization of Parabolic Equations in One Space Variable Siam Journal On Scientific and Statistical Computing. 11: 1-32. DOI: 10.1137/0911001 |
0.372 |
|
| 1989 |
Skeel RD. Waveform Iteration and the Shifted Picard Splitting Siam Journal On Scientific and Statistical Computing. 10: 756-776. DOI: 10.1137/0910046 |
0.416 |
|
| 1989 |
Skeel RD. The second-order backward differentiation formula is unconditionally zero-stable Applied Numerical Mathematics. 5: 145-149. DOI: 10.1016/0168-9274(89)90030-5 |
0.393 |
|
| 1986 |
Skeel RD. Construction of variable-stepsize multistep formulas Mathematics of Computation. 47: 503-510. DOI: 10.2307/2008169 |
0.33 |
|
| 1986 |
Skeel RD, Vu TV. Note on Blended Linear Multistep Formulas Acm Transactions On Mathematical Software (Toms). 12: 223-224. DOI: 10.1145/7921.7925 |
0.324 |
|
| 1986 |
Skeel RD. The Order of Accuracy for Deferred Corrections Using Uncentered End Formulas Siam Journal On Numerical Analysis. 23: 393-402. DOI: 10.1137/0723026 |
0.375 |
|
| 1986 |
Skeel RD. Thirteen ways to estimate global error Numerische Mathematik. 48: 1-20. DOI: 10.1007/Bf01389440 |
0.319 |
|
| 1982 |
Skeel RD. A Theoretical Framework for Proving Accuracy Results for Deferred Corrections Siam Journal On Numerical Analysis. 19: 171-196. DOI: 10.1137/0719009 |
0.346 |
|
| 1981 |
Skeel RD. Accuracy of point cyclic reductions for poisson's equation Journal of Computational Physics. 44: 198-205. DOI: 10.1016/0021-9991(81)90045-0 |
0.347 |
|
| 1980 |
Skeel RD. Iterative refinement implies numerical stability for gaussian elimination Mathematics of Computation. 35: 817-832. DOI: 10.1090/S0025-5718-1980-0572859-4 |
0.336 |
|
| 1979 |
Skeel RD. Scaling for Numerical Stability in Gaussian Elimination Journal of the Acm (Jacm). 26: 494-526. DOI: 10.1145/322139.322148 |
0.312 |
|
| 1979 |
Skeel RD. Equivalent forms of multistep formulas Mathematics of Computation. 33: 1229-1250. DOI: 10.1090/S0025-5718-1979-0537967-4 |
0.315 |
|
| 1977 |
Skeel RD, Kong AK. Blended Linear Multistep Methods Acm Transactions On Mathematical Software (Toms). 3: 326-345. DOI: 10.1145/355759.355762 |
0.37 |
|
| 1977 |
Skeel RD, Jackson LW. Consistency of Nordsieck Methods Siam Journal On Numerical Analysis. 14: 910-924. DOI: 10.1137/0714061 |
0.32 |
|
| 1976 |
Skeel R. Analysis of Fixed-Stepsize Methods Siam Journal On Numerical Analysis. 13: 664-685. DOI: 10.1137/0713055 |
0.371 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 2021 |
Kaya H, Hardy DJ, Skeel RD. Multilevel summation for periodic electrostatics using B-splines. The Journal of Chemical Physics. 154: 144105. PMID 33858159 DOI: 10.1063/5.0040925 |
0.295 |
|
| 1989 |
Skeel RD. Global error estimation and the backward differentiation formulas Applied Mathematics and Computation. 31: 197-208. DOI: 10.1145/101007.101030 |
0.286 |
|
| 1983 |
Skeel RD, Jackson LW. The Stability of Variable-Stepsize Nordsieck Methods Siam Journal On Numerical Analysis. 20: 840-853. DOI: 10.1137/0720056 |
0.28 |
|
| 1995 |
Nelson M, Humphrey W, Kufrin R, Gursoy A, Dalke A, Kale L, Skeel R, Schulten K. MDScope — a visual computing environment for structural biology Computer Physics Communications. 91: 111-133. DOI: 10.1016/0010-4655(95)00045-H |
0.279 |
|
| 1998 |
Skeel RD. Comments on Numerical Instability due to Varying Time Steps in Explicit Wave Propagation and Mechanics Calculations Journal of Computational Physics. 145: 758-759. DOI: 10.1006/Jcph.1998.6072 |
0.278 |
|
| 2011 |
Dadarlat VM, Skeel RD. Dual role of protein phosphorylation in DNA activator/coactivator binding. Biophysical Journal. 100: 469-77. PMID 21244843 DOI: 10.1016/J.Bpj.2010.11.053 |
0.277 |
|
| 2016 |
Fang Y, Sanz-Serna JM, Skeel RD. Erratum: "Compressible generalized hybrid Monte Carlo" [J. Chem. Phys. 140, 174108 (2014)]. The Journal of Chemical Physics. 144: 029901. PMID 26772590 DOI: 10.1063/1.4940219 |
0.272 |
|
| 2003 |
Ma Q, Izaguirre JA, Skeel RD. Nonlinear instability in multiple time stepping molecular dynamics Proceedings of the Acm Symposium On Applied Computing. 167-171. |
0.264 |
|
| 2019 |
Sarkar D, Vant J, Shekhar M, Richardson JS, Skeel R, Singharoy A. MDFF Error Analysis: A Tool for Determining Stereochemical and Thermodynamic Correct Structures Biophysical Journal. 116: 140a-141a. DOI: 10.1016/J.Bpj.2018.11.780 |
0.26 |
|
| 1986 |
Skeel RD. Supplement to Construction of Variable-Stepsize Multistep Formulas Mathematics of Computation. 47: S45. DOI: 10.2307/2008205 |
0.259 |
|
| 1981 |
Skeel RD. Effect of Equilibration on Residual Size for Partial Pivoting Siam Journal On Numerical Analysis. 18: 449-454. DOI: 10.1137/0718029 |
0.253 |
|
| 2015 |
Skeel RD. Comments on “A critical appraisal of Markov state models” by M. Sarich and C. Schütte European Physical Journal: Special Topics. 224: 2521-2523. DOI: 10.1140/Epjst/E2015-02539-Y |
0.246 |
|
| 2012 |
Huang H, Zhao R, Dickson BM, Skeel RD, Post CB. αC helix as a switch in the conformational transition of Src/CDK-like kinase domains. The Journal of Physical Chemistry. B. 116: 4465-75. PMID 22448785 DOI: 10.1021/Jp301628R |
0.232 |
|
| 1995 |
Skeel RD. Numerical Hamiltonian Problems (J. M. Sanz-Serna and M. P. Calvo) Siam Review. 37: 277-279. DOI: 10.1137/1037075 |
0.231 |
|
| 2020 |
Phillips JC, Hardy DJ, Maia JDC, Stone JE, Ribeiro JV, Bernardi RC, Buch R, Fiorin G, Hénin J, Jiang W, McGreevy R, Melo MCR, Radak BK, Skeel RD, Singharoy A, et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of Chemical Physics. 153: 044130. PMID 32752662 DOI: 10.1063/5.0014475 |
0.216 |
|
| 2020 |
Sanders T, Platte RB, Skeel RD. Effective new methods for automated parameter selection in regularized inverse problems Applied Numerical Mathematics. 152: 29-48. DOI: 10.1016/J.Apnum.2020.01.015 |
0.208 |
|
| 1997 |
Bishop TC, Skeel RD, Schulten K. Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics Journal of Computational Chemistry. 18: 1785-1791. DOI: 10.1002/(SICI)1096-987X(19971115)18:14<1785::AID-JCC7>3.0.CO;2-G |
0.193 |
|
| 2020 |
Vant JW, Sarkar D, Streitwieser E, Fiorin G, Skeel R, Vermaas JV, Singharoy A. Data-guided Multi-Map variables for ensemble refinement of molecular movies. The Journal of Chemical Physics. 153: 214102. PMID 33291927 DOI: 10.1063/5.0022433 |
0.191 |
|
| 1996 |
Nelson MT, Humphrey W, Gursoy A, Dalke A, Kale LV, Skeel RD, Schulten K. NAMD: A parallel, object-oriented molecular dynamics program International Journal of High Performance Computing Applications. 10: 251-268. |
0.189 |
|
| 2010 |
Skeel RD. Fast N-body methods: Why, what, and which Aip Conference Proceedings. 1281: 27-30. DOI: 10.1063/1.3498450 |
0.165 |
|
| 2009 |
Skeel RD. Two-point boundary value problems for curves: The case of minimum free energy paths1 Aip Conference Proceedings. 1168: 29-31. DOI: 10.1063/1.3241454 |
0.134 |
|
| 1986 |
Skeel RD, Bohmer K, Stetter HJ. Defect Correction Methods--Theory and Applications. Mathematics of Computation. 47: 374. DOI: 10.2307/2008106 |
0.122 |
|
| 1996 |
Nelson MT, Humphrey W, Gursoy A, Dalke A, Kalé LV, Skeel RD, Schulten K. NAMD: a Parallel, Object-Oriented Molecular Dynamics Program The International Journal of Supercomputer Applications and High Performance Computing. 10: 251-268. DOI: 10.1177/109434209601000401 |
0.105 |
|
| 2006 |
Leimkuhler B, Chipot C, Elber R, Laaksonen A, Mark A, Schlick T, Schütte C, Skeel R. New Algorithms for Macromolecular Simulation Lecture Notes in Computational Science and Engineering. 49. |
0.103 |
|
| 2011 |
Skeel RD, Zhao R. Solving geometric two-point boundary value problems Aip Conference Proceedings. 1389: 30-33. DOI: 10.1063/1.3636663 |
0.099 |
|
| 2014 |
Ding N, Fang Y, Babbush R, Chen C, Skeel RD, Neven H. Bayesian sampling using stochastic gradient thermostats Advances in Neural Information Processing Systems. 4: 3203-3211. |
0.093 |
|
| 1994 |
Board JA, Kalé LV, Schulten K, Skeel RD, Schlick T. Modeling Biomolecules: Larger Scales, Longer Durations Ieee Computational Science and Engineering. 1: 19-30. DOI: 10.1109/99.338771 |
0.053 |
|
| 1986 |
Skeel RD. Corrigendum: ‘‘Equivalent forms of multistep formulas” [Math.\ Comp.\ {\bf 33} (1979), no.\ 148, 1229–1250; MR0537967 (80j:65027)] Mathematics of Computation. 47: 769. DOI: 10.1090/S0025-5718-1986-0856720-9 |
0.051 |
|
| 2010 |
Skeel RD. Towards a definition of equilibration for markov chains Journal of Numerical Analysis, Industrial and Applied Mathematics. 5: 103-111. |
0.026 |
|
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