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Volumn 225, Issue 1, 2007, Pages 1-5

Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations

Author keywords

Ewald sum; Force fields; Molecular dynamics

Indexed keywords

DYNAMICS SIMULATION; ENERGY; EWALD SUMS; FORCE CALCULATION; FORCEFIELDS;

EID: 34447255444     PISSN: 00219991     EISSN: 10902716     Source Type: Journal    
DOI: 10.1016/j.jcp.2007.03.010     Document Type: Article
Times cited : (27)

References (19)
  • 3
    • 28144464582 scopus 로고
    • Multilevel matrix multiplication and fast solution of integral equations
    • Brandt A., and Lubrecht A.A. Multilevel matrix multiplication and fast solution of integral equations. J. Comput. Phys. 90 (1990) 348-370
    • (1990) J. Comput. Phys. , vol.90 , pp. 348-370
    • Brandt, A.1    Lubrecht, A.A.2
  • 4
    • 0037197257 scopus 로고    scopus 로고
    • Multiple grid methods for classical molecular dynamics
    • Skeel R.D., Tezcan I., and Hardy D.J. Multiple grid methods for classical molecular dynamics. J. Comput. Chem. 23 6 (2002) 673-684
    • (2002) J. Comput. Chem. , vol.23 , Issue.6 , pp. 673-684
    • Skeel, R.D.1    Tezcan, I.2    Hardy, D.J.3
  • 5
    • 85190784862 scopus 로고    scopus 로고
    • D. J. Hardy, Multilevel summation for the fast evaluation of forces for the simulation of biomolecules, Ph.D. Thesis, University of Illinois at Urbana-Champaign, also Department of Computer Science Report No. UIUCDCS-R-2006-2546, May 2006. Available online at http://www.cs.uiuc.edu/research/techreports.php?year=2006.
  • 6
    • 0035339718 scopus 로고    scopus 로고
    • Multiscale fast summation of long range charge and dipolar interactions
    • Sandak B. Multiscale fast summation of long range charge and dipolar interactions. J. Comput. Chem. 22 7 (2001) 717-731
    • (2001) J. Comput. Chem. , vol.22 , Issue.7 , pp. 717-731
    • Sandak, B.1
  • 7
    • 0000396658 scopus 로고
    • A fast algorithm for particle simulations
    • Greengard L., and Rokhlin V. A fast algorithm for particle simulations. J. Comput. Phys. 73 (1987) 325-348
    • (1987) J. Comput. Phys. , vol.73 , pp. 325-348
    • Greengard, L.1    Rokhlin, V.2
  • 8
    • 0000316648 scopus 로고    scopus 로고
    • Difficulties with multiple timestepping and the fast multipole algorithm in molecular dynamics
    • Bishop T., Skeel R.D., and Schulten K. Difficulties with multiple timestepping and the fast multipole algorithm in molecular dynamics. J. Comput. Chem. 18 14 (1997) 1785-1791
    • (1997) J. Comput. Chem. , vol.18 , Issue.14 , pp. 1785-1791
    • Bishop, T.1    Skeel, R.D.2    Schulten, K.3
  • 9
    • 0030172529 scopus 로고    scopus 로고
    • 3M, FMM, and the Ewald method for large periodic Coulombic systems
    • 3M, FMM, and the Ewald method for large periodic Coulombic systems. Comput. Phys. Commun. 95 2 and 3 (1996) 93-110
    • (1996) Comput. Phys. Commun. , vol.95 , Issue.2-3 , pp. 93-110
    • Pollock, E.L.1    Glosli, J.2
  • 10
    • 22244433235 scopus 로고    scopus 로고
    • How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines
    • Deserno M., and Holm C. How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines. J. Chem. Phys. 109 18 (1998) 7678-7693
    • (1998) J. Chem. Phys. , vol.109 , Issue.18 , pp. 7678-7693
    • Deserno, M.1    Holm, C.2
  • 11
    • 0034506266 scopus 로고    scopus 로고
    • Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions
    • Toukmaji A., Sagui C., Board J., and Darden T. Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions. J. Chem. Phys. 113 24 (2000) 10913-10927
    • (2000) J. Chem. Phys. , vol.113 , Issue.24 , pp. 10913-10927
    • Toukmaji, A.1    Sagui, C.2    Board, J.3    Darden, T.4
  • 12
    • 85190817969 scopus 로고    scopus 로고
    • W. Wang, Fast polarizable force field computation in biomolecular simulations, Ph.D. Thesis, University of Illinois at Urbana-Champaign, also Department of Computer Science Report No. UIUCDCS-R-2005-2522, 2005. Available online at http://www.cs.uiuc.edu/research/techreports.php?year=2005.
  • 14
    • 84986440341 scopus 로고
    • SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water molecules
    • Miyamoto S., and Kollman P.A. SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water molecules. J. Comput. Chem. 13 8 (1992) 952-962
    • (1992) J. Comput. Chem. , vol.13 , Issue.8 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 15
    • 18144377695 scopus 로고    scopus 로고
    • Monitoring energy drift with shadow Hamiltonians
    • Engle R.D., Skeel R.D., and Drees M. Monitoring energy drift with shadow Hamiltonians. J. Comput. Phys. 206 2 (2005) 432-452
    • (2005) J. Comput. Phys. , vol.206 , Issue.2 , pp. 432-452
    • Engle, R.D.1    Skeel, R.D.2    Drees, M.3
  • 16
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equation of motion of a system with constraints: molecular dynamics of n-alkanes
    • Ryckaert J., Ciccotti G., and Berendsen H. Numerical integration of the cartesian equation of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23 (1977) 327-341
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.1    Ciccotti, G.2    Berendsen, H.3
  • 17
    • 33646650705 scopus 로고
    • Reversible multiple time scale molecular dynamics
    • Tuckerman M., Berne B.J., and Martyna G.J. Reversible multiple time scale molecular dynamics. J. Chem. Phys. 97 3 (1992) 1990-2001
    • (1992) J. Chem. Phys. , vol.97 , Issue.3 , pp. 1990-2001
    • Tuckerman, M.1    Berne, B.J.2    Martyna, G.J.3
  • 18
    • 84963146276 scopus 로고
    • Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions
    • Grubmüller H., Heller H., Windemuth A., and Schulten K. Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Mol. Simul. 6 (1991) 121-142
    • (1991) Mol. Simul. , vol.6 , pp. 121-142
    • Grubmüller, H.1    Heller, H.2    Windemuth, A.3    Schulten, K.4
  • 19
    • 85190791564 scopus 로고    scopus 로고
    • http://www.ks.uiuc.edu/Research/namd/.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.