Change search
ReferencesLink to record
Permanent link

Direct link
Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation
Show others and affiliations
Number of Authors: 6
2015 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 12, 5737-5746 p.Article in journal (Refereed) Published
Abstract [en]

Long-range lattice summation techniques such as the particle-mesh Ewald (PME) algorithm for electrostatics have been revolutionary to the precision and accuracy of molecular simulations in general. Despite the performance penalty associated with lattice summation electrostatics, few biomolecular simulations today are performed without it. There are increasingly strong arguments for moving in the same direction for Lennard-Jones (LJ) interactions, and by using geometric approximations of the combination rules in reciprocal space, we have been able to make a very high-performance implementation available in GROMACS. Here, we present a new way to correct for these approximations to achieve exact treatment of Lorentz-Berthelot combination rules within the cutoff, and only a very small approximation error remains outside the cutoff (a part that would be completely ignored without LJ-PME). This not only improves accuracy by almost an order of magnitude but also achieves absolute biomolecular simulation performance that is an order of magnitude faster than any other available lattice summation technique for LJ interactions. The implementation includes both CPU and GPU acceleration, and its combination with improved scaling LJ-PME simulations now provides performance close to the truncated potential methods in GROMACS but with much higher accuracy.

Place, publisher, year, edition, pages
2015. Vol. 11, no 12, 5737-5746 p.
National Category
Chemical Sciences Physical Sciences
Identifiers
URN: urn:nbn:se:su:diva-125665DOI: 10.1021/acs.jctc.5b00726ISI: 000366223400017PubMedID: 26587968OAI: oai:DiVA.org:su-125665DiVA: diva2:894666
Available from: 2016-01-15 Created: 2016-01-15 Last updated: 2016-01-15Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Lindahl, Erik
By organisation
Department of Biochemistry and Biophysics
In the same journal
Journal of Chemical Theory and Computation
Chemical SciencesPhysical Sciences

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 12 hits
ReferencesLink to record
Permanent link

Direct link