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Core Information
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| Title: |
Efficient sampling of ion motions in molecular dynamics simulations: Variant Hamiltonian replica exchange method |
| Abstract: |
Counterions play an important role in biomolecular functions. Although molecular dynamics simulations have been applied on various nucleic acids, accurate and efficient descriptions of ion motions around DNA or RNA are still challenging, largely due to ions’ slow mobility. Here, a variant Hamiltonian replica exchange method was developed to achieve efficient sampling of ion motions. Based on the present approach, the results from our model study on classical Drew–Dickerson B-DNA dodecamer show remarkable agreements with experimental measurements and nonlinear Poisson–Boltzmann predictions. Due to the employment of this variant Hamiltonian replica exchange method, these amazing agreements can be achieved within a short simulation time (900 ps).
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| Keywords: |
Ion motion, Hamiltonian replica exchange, sampling, molecular dynamics |
Author Information
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| 1. | Min, Donghong | [ FSU/SCS ] | Post doc | | 2. | Li, Hongzhi | [ FSU/SCS ] | Post doc | | 3. | Li, Guohui | [ FSU/SCS ] | Post doc | | 4. | Berg, Bernd | [ FSU/SCS ] | Neither | | 5. | Fenley, Marcia | [ FSU/IMB ] | Neither | | 6. | Yang, Wei | [ FSU/SCS ] | Neither |
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Detailed Scientific Article Information
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| Journal Name: |
Chemical Physics Letters |
| Volume: |
454 |
| Page Range: |
391-395 |
Article Number: |
Not Provided |
| Number of Pages: |
Not Provided |
| Year of Publication: |
2008 |
| Refereed: |
Yes |
| Digital Object Identifier (DOI), if available: |
doi:10.1016/j.cplett.2008.02.055 |
| Official Url: |
Not Provided |
| ISSN: |
Not Provided |
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Subjects Information
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1. Biology
2. Chemistry
3. Physics
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