Computer simulation of urea-water mixtures: A test of force field parameters for use in biomolecular simulation
A molecular model for urea to be used in conjunction with the simple point charge (SPC) model for liquid water in protein denaturation studies is validated by comparison of molecular dynamics (MD) simulation results to experimental data at 298 K as a function of urea mole fraction. The density, enth...
| Main Authors: | , , |
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| Format: | Journal article |
| Language: | English |
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2004
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| _version_ | 1797094356599963648 |
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| author | Smith, L Berendsen, H van Gunsteren, W |
| author_facet | Smith, L Berendsen, H van Gunsteren, W |
| author_sort | Smith, L |
| collection | OXFORD |
| description | A molecular model for urea to be used in conjunction with the simple point charge (SPC) model for liquid water in protein denaturation studies is validated by comparison of molecular dynamics (MD) simulation results to experimental data at 298 K as a function of urea mole fraction. The density, enthalpy of mixing, free enthalpy of urea hydration, and urea diffusion show very good agreement with the experimental values. The experimental error in the free enthalpy of hydration, which is dominated by the inaccuracy of the vapor pressure of solid urea, is larger than the simulation error. This limited accuracy does not allow a check of the nonideality of the solution. Free enthalpies have been obtained by thermodynamic integration. The importance of a correct use of the combinatorial factor in the partition function when interpreting simulation results obtained by thermodynamic integration is discussed. The tested, GROMOS96 compatible, force field parameters form a good basis for biomolecular simulations using urea-water mixtures. |
| first_indexed | 2024-03-07T04:12:58Z |
| format | Journal article |
| id | oxford-uuid:c8747ef5-1954-4f7b-84f4-9b79b9416ee4 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T04:12:58Z |
| publishDate | 2004 |
| record_format | dspace |
| spelling | oxford-uuid:c8747ef5-1954-4f7b-84f4-9b79b9416ee42022-03-27T06:52:16ZComputer simulation of urea-water mixtures: A test of force field parameters for use in biomolecular simulationJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:c8747ef5-1954-4f7b-84f4-9b79b9416ee4EnglishSymplectic Elements at Oxford2004Smith, LBerendsen, Hvan Gunsteren, WA molecular model for urea to be used in conjunction with the simple point charge (SPC) model for liquid water in protein denaturation studies is validated by comparison of molecular dynamics (MD) simulation results to experimental data at 298 K as a function of urea mole fraction. The density, enthalpy of mixing, free enthalpy of urea hydration, and urea diffusion show very good agreement with the experimental values. The experimental error in the free enthalpy of hydration, which is dominated by the inaccuracy of the vapor pressure of solid urea, is larger than the simulation error. This limited accuracy does not allow a check of the nonideality of the solution. Free enthalpies have been obtained by thermodynamic integration. The importance of a correct use of the combinatorial factor in the partition function when interpreting simulation results obtained by thermodynamic integration is discussed. The tested, GROMOS96 compatible, force field parameters form a good basis for biomolecular simulations using urea-water mixtures. |
| spellingShingle | Smith, L Berendsen, H van Gunsteren, W Computer simulation of urea-water mixtures: A test of force field parameters for use in biomolecular simulation |
| title | Computer simulation of urea-water mixtures: A test of force field parameters for use in biomolecular simulation |
| title_full | Computer simulation of urea-water mixtures: A test of force field parameters for use in biomolecular simulation |
| title_fullStr | Computer simulation of urea-water mixtures: A test of force field parameters for use in biomolecular simulation |
| title_full_unstemmed | Computer simulation of urea-water mixtures: A test of force field parameters for use in biomolecular simulation |
| title_short | Computer simulation of urea-water mixtures: A test of force field parameters for use in biomolecular simulation |
| title_sort | computer simulation of urea water mixtures a test of force field parameters for use in biomolecular simulation |
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