SimTK: Project category

RNA

Biocomputational methods complement experimental techniques to expand our understanding of RNA, molecules vital to the normal expression of genes within our bodies.

News

Publications

P. Eastman, J. Swails, J. D. Chodera, R. T. McGibbon, Y. Zhao, K. A. Beauchamp, L.-P. Wang, A. C. Simmonett, M. P. Harrigan, C. D. Stern, R. P. Wiewiora, B. R. Brooks, and V. S. Pande. "OpenMM 7: Rapid development of high performance algorithms for molecular dynamics." PLOS Comp. Biol. 13(7): e1005659.

Tek, A., Korostelev, A.A. and Flores, S.C. (2015) MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory. Nucleic Acids Res., 10.1093/nar/gkv1457.

Wang, L-P., Martinez, T. J. and Pande, V.S. "Building force fields - an automatic, systematic and reproducible approach", submitted.

Discussion

Re: Does the neighbor list update when setPositions is called using C++ API?

OpenMM Nov 15, 2024

Re: Setting up Dual Topology Files for Mutation Alchemical Free Perturbation

OpenMM Nov 13, 2024

Re: Reflective wall to prevent water from penetrating the lipid bilayer

OpenMM Nov 12, 2024

SimTK is maintained through Grant R01GM124443 01A1 from the National Institutes of Health (NIH). It was initially developed as part of the Simbios project funded by the NIH as part of the NIH Roadmap for Medical Research, Grant U54 GM072970.

Version 4.2.2. Website design by Viewfarm. Icons created by SimTK team using art by GraphBerry from www.flaticon.com under a CC BY 3.0 license. Forked from FusionForge 6.0.5.

Featured projects

Recently updated projects

News

New package added: MMB 3.14 for Windows

ForceBalance version 1.7.0 released!

OpenSim gets high marks as a multibody system simulator

Publications

Discussion

Re: Does the neighbor list update when setPositions is called using C++ API?

Re: Setting up Dual Topology Files for Mutation Alchemical Free Perturbation

Re: Reflective wall to prevent water from penetrating the lipid bilayer