A mathematical approach to smoothed molecular dynamics: correcting potentials for freezing bond angles
Abstract: "The interaction potential of molecular systems which are typically used in molecular dynamics can be split into two parts of essentially different stiffness. The strong part of the potential forces the solution of the equations of motion to oscillate on a very small time scale. There...
Gespeichert in:
| Hauptverfasser: | , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Berlin-Wilmersdorf
1995
|
| Schriftenreihe: | Konrad-Zuse-Zentrum für Informationstechnik <Berlin>: Preprint SC
1995,30 |
| Schlagworte: | |
| Zusammenfassung: | Abstract: "The interaction potential of molecular systems which are typically used in molecular dynamics can be split into two parts of essentially different stiffness. The strong part of the potential forces the solution of the equations of motion to oscillate on a very small time scale. There is a strong need for eliminating the smallest time scales because they are a severe restriction for numerical long-term simulations of macromolecules. This leads to the idea of just freezing the high frequency degrees of freedom (bond stretching and bond angles). However, the naive way of doing this via holonomic constraints is bound to produce incorrect results. The paper presents a mathematically rigorous discussion of the limit situation in which the stiffness of the strong part of the potential is increased to infinity. It is demonstrated that the average of the limit solution indeed obeys a constrained Hamiltonian system but with a corrected soft potential. An explicit formula for the additive potential correction is given and its significant contribution is demonstrated in an illustrative example. It appears that this correcting potential is definitely not identical with the Fixman-potential as was repeatedly assumed in the literature." |
| Beschreibung: | 23 S. |
Internformat
MARC
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| 100 | 1 | |a Bornemann, Folkmar |d 1967- |e Verfasser |0 (DE-588)120096269 |4 aut | |
| 245 | 1 | 0 | |a A mathematical approach to smoothed molecular dynamics |b correcting potentials for freezing bond angles |c Folkmar A. Bornemann ; Christof Schütte |
| 264 | 1 | |a Berlin-Wilmersdorf |c 1995 | |
| 300 | |a 23 S. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a Konrad-Zuse-Zentrum für Informationstechnik <Berlin>: Preprint SC |v 1995,30 | |
| 520 | 3 | |a Abstract: "The interaction potential of molecular systems which are typically used in molecular dynamics can be split into two parts of essentially different stiffness. The strong part of the potential forces the solution of the equations of motion to oscillate on a very small time scale. There is a strong need for eliminating the smallest time scales because they are a severe restriction for numerical long-term simulations of macromolecules. This leads to the idea of just freezing the high frequency degrees of freedom (bond stretching and bond angles). However, the naive way of doing this via holonomic constraints is bound to produce incorrect results. The paper presents a mathematically rigorous discussion of the limit situation in which the stiffness of the strong part of the potential is increased to infinity. It is demonstrated that the average of the limit solution indeed obeys a constrained Hamiltonian system but with a corrected soft potential. An explicit formula for the additive potential correction is given and its significant contribution is demonstrated in an illustrative example. It appears that this correcting potential is definitely not identical with the Fixman-potential as was repeatedly assumed in the literature." | |
| 650 | 4 | |a Hamiltonian systems | |
| 650 | 4 | |a Molecular dynamics | |
| 700 | 1 | |a Schütte, Christof |d 1966- |e Verfasser |0 (DE-588)1049564030 |4 aut | |
| 830 | 0 | |a Konrad-Zuse-Zentrum für Informationstechnik <Berlin>: Preprint SC |v 1995,30 |w (DE-604)BV004801715 |9 1995,30 | |
| 943 | 1 | |a oai:aleph.bib-bvb.de:BVB01-007142528 | |
Datensatz im Suchindex
| _version_ | 1820882503277215744 |
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| author | Bornemann, Folkmar 1967- Schütte, Christof 1966- |
| author_GND | (DE-588)120096269 (DE-588)1049564030 |
| author_facet | Bornemann, Folkmar 1967- Schütte, Christof 1966- |
| author_role | aut aut |
| author_sort | Bornemann, Folkmar 1967- |
| author_variant | f b fb c s cs |
| building | Verbundindex |
| bvnumber | BV010700891 |
| classification_rvk | SS 4777 |
| ctrlnum | (OCoLC)35423799 (DE-599)BVBBV010700891 |
| discipline | Informatik |
| format | Book |
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| id | DE-604.BV010700891 |
| illustrated | Not Illustrated |
| indexdate | 2025-01-10T17:07:56Z |
| institution | BVB |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-007142528 |
| oclc_num | 35423799 |
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| owner | DE-12 DE-703 |
| owner_facet | DE-12 DE-703 |
| physical | 23 S. |
| publishDate | 1995 |
| publishDateSearch | 1995 |
| publishDateSort | 1995 |
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| series | Konrad-Zuse-Zentrum für Informationstechnik <Berlin>: Preprint SC |
| series2 | Konrad-Zuse-Zentrum für Informationstechnik <Berlin>: Preprint SC |
| spelling | Bornemann, Folkmar 1967- Verfasser (DE-588)120096269 aut A mathematical approach to smoothed molecular dynamics correcting potentials for freezing bond angles Folkmar A. Bornemann ; Christof Schütte Berlin-Wilmersdorf 1995 23 S. txt rdacontent n rdamedia nc rdacarrier Konrad-Zuse-Zentrum für Informationstechnik <Berlin>: Preprint SC 1995,30 Abstract: "The interaction potential of molecular systems which are typically used in molecular dynamics can be split into two parts of essentially different stiffness. The strong part of the potential forces the solution of the equations of motion to oscillate on a very small time scale. There is a strong need for eliminating the smallest time scales because they are a severe restriction for numerical long-term simulations of macromolecules. This leads to the idea of just freezing the high frequency degrees of freedom (bond stretching and bond angles). However, the naive way of doing this via holonomic constraints is bound to produce incorrect results. The paper presents a mathematically rigorous discussion of the limit situation in which the stiffness of the strong part of the potential is increased to infinity. It is demonstrated that the average of the limit solution indeed obeys a constrained Hamiltonian system but with a corrected soft potential. An explicit formula for the additive potential correction is given and its significant contribution is demonstrated in an illustrative example. It appears that this correcting potential is definitely not identical with the Fixman-potential as was repeatedly assumed in the literature." Hamiltonian systems Molecular dynamics Schütte, Christof 1966- Verfasser (DE-588)1049564030 aut Konrad-Zuse-Zentrum für Informationstechnik <Berlin>: Preprint SC 1995,30 (DE-604)BV004801715 1995,30 |
| spellingShingle | Bornemann, Folkmar 1967- Schütte, Christof 1966- A mathematical approach to smoothed molecular dynamics correcting potentials for freezing bond angles Konrad-Zuse-Zentrum für Informationstechnik <Berlin>: Preprint SC Hamiltonian systems Molecular dynamics |
| title | A mathematical approach to smoothed molecular dynamics correcting potentials for freezing bond angles |
| title_auth | A mathematical approach to smoothed molecular dynamics correcting potentials for freezing bond angles |
| title_exact_search | A mathematical approach to smoothed molecular dynamics correcting potentials for freezing bond angles |
| title_full | A mathematical approach to smoothed molecular dynamics correcting potentials for freezing bond angles Folkmar A. Bornemann ; Christof Schütte |
| title_fullStr | A mathematical approach to smoothed molecular dynamics correcting potentials for freezing bond angles Folkmar A. Bornemann ; Christof Schütte |
| title_full_unstemmed | A mathematical approach to smoothed molecular dynamics correcting potentials for freezing bond angles Folkmar A. Bornemann ; Christof Schütte |
| title_short | A mathematical approach to smoothed molecular dynamics |
| title_sort | a mathematical approach to smoothed molecular dynamics correcting potentials for freezing bond angles |
| title_sub | correcting potentials for freezing bond angles |
| topic | Hamiltonian systems Molecular dynamics |
| topic_facet | Hamiltonian systems Molecular dynamics |
| volume_link | (DE-604)BV004801715 |
| work_keys_str_mv | AT bornemannfolkmar amathematicalapproachtosmoothedmoleculardynamicscorrectingpotentialsforfreezingbondangles AT schuttechristof amathematicalapproachtosmoothedmoleculardynamicscorrectingpotentialsforfreezingbondangles |