Testing the inter-operability of the CHARMM and SPC/Fw force fields for conformational sampling

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.

Keywords::

• force field
• biomolecule
• water
• replica exchange

Acknowledgements

This work was supported by the Engineering and Physical Sciences Research Council (Grant number EP/I001514/1). This Programme Grant funds the Materials Interface with Biology (MIB) consortium. The authors wish to thank the Centre for Scientific Computing, University of Warwick for computing resource. TRW thanks veski for an Innovation Fellowship. The authors also thank Ms Louise Wright for assistance with the Ramachandran plotting.