Improved sampling for simulations of interfacial membrane proteins: application of generalized shadow hybrid Monte Carlo to a peptide toxin/bilayer system.
The computational costs associated with performing molecular dynamics (MD) simulations are still somewhat prohibitive and therefore limit the time and length scales that can be currently achieved. One approach to overcoming the limited size and duration of a simulation is to reduce the amount of det...
| Main Authors: | , , , |
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| Format: | Journal article |
| Language: | English |
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2008
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| _version_ | 1797072173210271744 |
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| author | Wee, C Sansom, MS Reich, S Akhmatskaya, E |
| author_facet | Wee, C Sansom, MS Reich, S Akhmatskaya, E |
| author_sort | Wee, C |
| collection | OXFORD |
| description | The computational costs associated with performing molecular dynamics (MD) simulations are still somewhat prohibitive and therefore limit the time and length scales that can be currently achieved. One approach to overcoming the limited size and duration of a simulation is to reduce the amount of detail when representing a system of interest, generally termed "coarse-graining". An alternative approach is via more efficient sampling methods that offer an enhanced search of a complex multidimensional energy landscape. One could also combine enhanced sampling methods with a coarse-grained (CG) force field. Here, we apply generalized shadow hybrid Monte Carlo (GSHMC), a recently proposed simulation protocol, to a biomolecular system of moderate size and show that GSHMC offers improved sampling compared to standard MD simulation. Our test system is a CG representation of a small peptide toxin interacting with a phospholipid bilayer. Specifically, we show that GSHMC allows for a quicker localization of the toxin to its equilibrium location of interaction at the headgroup/water interface of the bilayer. GSHMC therefore potentially allows for future exploration of larger and more complex systems over longer periods, which would otherwise be impractical to perform using conventional simulation methodology. |
| first_indexed | 2024-03-06T23:03:52Z |
| format | Journal article |
| id | oxford-uuid:631f70aa-9200-4a0d-a2c7-a54beeaee68b |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T23:03:52Z |
| publishDate | 2008 |
| record_format | dspace |
| spelling | oxford-uuid:631f70aa-9200-4a0d-a2c7-a54beeaee68b2022-03-26T18:10:41ZImproved sampling for simulations of interfacial membrane proteins: application of generalized shadow hybrid Monte Carlo to a peptide toxin/bilayer system.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:631f70aa-9200-4a0d-a2c7-a54beeaee68bEnglishSymplectic Elements at Oxford2008Wee, CSansom, MSReich, SAkhmatskaya, EThe computational costs associated with performing molecular dynamics (MD) simulations are still somewhat prohibitive and therefore limit the time and length scales that can be currently achieved. One approach to overcoming the limited size and duration of a simulation is to reduce the amount of detail when representing a system of interest, generally termed "coarse-graining". An alternative approach is via more efficient sampling methods that offer an enhanced search of a complex multidimensional energy landscape. One could also combine enhanced sampling methods with a coarse-grained (CG) force field. Here, we apply generalized shadow hybrid Monte Carlo (GSHMC), a recently proposed simulation protocol, to a biomolecular system of moderate size and show that GSHMC offers improved sampling compared to standard MD simulation. Our test system is a CG representation of a small peptide toxin interacting with a phospholipid bilayer. Specifically, we show that GSHMC allows for a quicker localization of the toxin to its equilibrium location of interaction at the headgroup/water interface of the bilayer. GSHMC therefore potentially allows for future exploration of larger and more complex systems over longer periods, which would otherwise be impractical to perform using conventional simulation methodology. |
| spellingShingle | Wee, C Sansom, MS Reich, S Akhmatskaya, E Improved sampling for simulations of interfacial membrane proteins: application of generalized shadow hybrid Monte Carlo to a peptide toxin/bilayer system. |
| title | Improved sampling for simulations of interfacial membrane proteins: application of generalized shadow hybrid Monte Carlo to a peptide toxin/bilayer system. |
| title_full | Improved sampling for simulations of interfacial membrane proteins: application of generalized shadow hybrid Monte Carlo to a peptide toxin/bilayer system. |
| title_fullStr | Improved sampling for simulations of interfacial membrane proteins: application of generalized shadow hybrid Monte Carlo to a peptide toxin/bilayer system. |
| title_full_unstemmed | Improved sampling for simulations of interfacial membrane proteins: application of generalized shadow hybrid Monte Carlo to a peptide toxin/bilayer system. |
| title_short | Improved sampling for simulations of interfacial membrane proteins: application of generalized shadow hybrid Monte Carlo to a peptide toxin/bilayer system. |
| title_sort | improved sampling for simulations of interfacial membrane proteins application of generalized shadow hybrid monte carlo to a peptide toxin bilayer system |
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