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Testing the inter-operability of the CHARMM and SPC/Fw force fields for conformational sampling
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Desmond, Jasmine L., Rodger, P. Mark and Walsh, Tiffany R. (2013) Testing the inter-operability of the CHARMM and SPC/Fw force fields for conformational sampling. Molecular Simulation, Volume 40 (Number 12). pp. 912-921. doi:10.1080/08927022.2013.824574
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Official URL: http://dx.doi.org/10.1080/08927022.2013.824574
Abstract
One of the challenges in the area of molecular simulation of biointerfaces is to ensure that the interatomic potentials used to describe such interfaces capture the essential chemistry and physics of the system. Here, we report the conformational testing of the inter-operability of the CHARMM and SPC/Fw force fields, the compatibility of which is essential for successful incorporation of a description of biomolecules into current biomineralisation force fields. The effect of the new water model, SPC/Fw, on the conformational equilibrium of two contrasting exemplar tripeptide sequences, RGD and SPT, as described by the CHARMM force field, has been probed by the analysis of results generated from replica-exchange molecular dynamics simulations. We compare the ensemble of conformational states generated from the CHARMM-SPC/Fw force fields with those obtained from the more typical CHARMM-TIPS3P combination. Analysis shows that the findings from the two force field combinations compare very favourably for equilibrium structure determination for both peptides.
| Item Type: | Journal Article | ||||||||
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| Divisions: | Faculty of Science > Chemistry Faculty of Science > Centre for Scientific Computing |
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| Journal or Publication Title: | Molecular Simulation | ||||||||
| Publisher: | Taylor & Francis Inc. | ||||||||
| ISSN: | 0892-7022 | ||||||||
| Official Date: | 3 September 2013 | ||||||||
| Dates: |
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| Volume: | Volume 40 | ||||||||
| Number: | Number 12 | ||||||||
| Number of Pages: | 10 | ||||||||
| Page Range: | pp. 912-921 | ||||||||
| DOI: | 10.1080/08927022.2013.824574 | ||||||||
| Status: | Peer Reviewed | ||||||||
| Publication Status: | Published | ||||||||
| Access rights to Published version: | Restricted or Subscription Access |
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