Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions
| dc.contributor.author | M. Fischer, Nina | |
| dc.contributor.author | J. van Maaren, Paul | |
| dc.contributor.author | C. Ditz, Jonas | |
| dc.contributor.author | Yildirim, Ahmet | |
| dc.contributor.author | van der Spoel, David | |
| dc.date.accessioned | 2019-11-28T10:47:04Z | |
| dc.date.available | 2019-11-28T10:47:04Z | |
| dc.date.issued | 2015 | en_US |
| dc.department | Beden Eğitimi ve Spor Yüksekokulu | en_US |
| dc.description.abstract | In order to increase the accuracy of classical computer simulations, existing methodologies may need to be adapted. Hitherto, most force fields employ a truncated potential function to model van der Waals interactions, sometimes augmented with an analytical correction. Although such corrections are accurate for homogeneous systems with a long cutoff, they should not be used in inherently inhomogeneous systems such as biomolecular and interface systems. For such cases, a variant of the particle mesh Ewald algorithm (Lennard-Jones PME) was already proposed 20 years ago (Essmann et al. J. Chem. Phys. 1995, 103, 8577-8593), but it was implemented only recently (Wennberg et al. J. Chem. Theory Comput. 2013, 9, 3527-3537) in a major simulation code (GROMACS). The availability of this method allows surface tensions of liquids as well as bulk properties to be established, such as density and enthalpy of vaporization, without approximations due to truncation. Here, we report on simulations of ≈150 liquids (taken from a force field benchmark: Caleman et al. J. Chem. Theory Comput. 2012, 8, 61-74) using three different force fields and compare simulations with and without explicit long-range van der Waals interactions. We find that the density and enthalpy of vaporization increase for most liquids using the generalized Amber force field (GAFF, Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) and the Charmm generalized force field (CGenFF, Vanommeslaeghe et al. J. Comput. Chem. 2010, 31, 671-690) but less so for OPLS/AA (Jorgensen and Tirado-Rives, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670), which was parametrized with an analytical correction to the van der Waals potential. The surface tension increases by ≈10(-2) N/m for all force fields. These results suggest that van der Waals attractions in force fields are too strong, in particular for the GAFF and CGenFF. In addition to the simulation results, we introduce a new version of a web server, http://virtualchemistry.org, aimed at facilitating sharing and reuse of input files for molecular simulations. | en_US |
| dc.description.provenance | Submitted by Ahmet Yıldırım (ahmedoyildirim@siirt.edu.tr) on 2019-11-28T10:47:04Z No. of bitstreams: 1 10.pdf: 1404617 bytes, checksum: d3e68a05cf0b95d3de5a7ffaab2094f3 (MD5) | en |
| dc.description.provenance | Made available in DSpace on 2019-11-28T10:47:04Z (GMT). No. of bitstreams: 1 10.pdf: 1404617 bytes, checksum: d3e68a05cf0b95d3de5a7ffaab2094f3 (MD5) Previous issue date: 2015 | en |
| dc.identifier.pmid | 26575731 | |
| dc.identifier.scopus | 2-s2.0-84944052564 | |
| dc.identifier.scopusquality | Q1 | |
| dc.identifier.uri | https://hdl.handle.net/20.500.12604/1878 | |
| dc.identifier.wos | WOS:000358104800005 | |
| dc.identifier.wosquality | Q1 | |
| dc.indekslendigikaynak | Web of Science | |
| dc.indekslendigikaynak | Scopus | |
| dc.indekslendigikaynak | PubMed | |
| dc.institutionauthor | Yildirim, Ahmet | |
| dc.language.iso | other | en_US |
| dc.relation.publicationcategory | Makale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı | en_US |
| dc.rights | info:eu-repo/semantics/openAccess | en_US |
| dc.snmz | KG_20241224 | |
| dc.title | Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions | en_US |
| dc.type | Article | en_US |
