Simmonett AC - Search Results

1

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS. Eastman P, et al. Among authors: simmonett ac. PLoS Comput Biol. 2017 Jul 26;13(7):e1005659. doi: 10.1371/journal.pcbi.1005659. eCollection 2017 Jul. PLoS Comput Biol. 2017. PMID: 28746339 Free PMC article.

2

An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald.

Simmonett AC, Pickard FC 4th, Schaefer HF 3rd, Brooks BR. Simmonett AC, et al. J Chem Phys. 2014 May 14;140(18):184101. doi: 10.1063/1.4873920. J Chem Phys. 2014. PMID: 24832247 Free PMC article.

3

Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions.

Mei Y, Simmonett AC, Pickard FC 4th, DiStasio RA Jr, Brooks BR, Shao Y. Mei Y, et al. Among authors: simmonett ac. J Phys Chem A. 2015 Jun 4;119(22):5865-82. doi: 10.1021/acs.jpca.5b03159. Epub 2015 May 18. J Phys Chem A. 2015. PMID: 25945749 Free PMC article.

4

Efficient treatment of induced dipoles.

Simmonett AC, Pickard FC 4th, Shao Y, Cheatham TE 3rd, Brooks BR. Simmonett AC, et al. J Chem Phys. 2015 Aug 21;143(7):074115. doi: 10.1063/1.4928530. J Chem Phys. 2015. PMID: 26298123 Free PMC article.

5

Molecular Multipole Potential Energy Functions for Water.

Tan ML, Tran KN, Pickard FC 4th, Simmonett AC, Brooks BR, Ichiye T. Tan ML, et al. Among authors: simmonett ac. J Phys Chem B. 2016 Mar 3;120(8):1833-42. doi: 10.1021/acs.jpcb.5b09565. Epub 2015 Nov 24. J Phys Chem B. 2016. PMID: 26562223

6

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method.

König G, Mei Y, Pickard FC 4th, Simmonett AC, Miller BT, Herbert JM, Woodcock HL, Brooks BR, Shao Y. König G, et al. Among authors: simmonett ac. J Chem Theory Comput. 2016 Jan 12;12(1):332-44. doi: 10.1021/acs.jctc.5b00874. Epub 2015 Dec 11. J Chem Theory Comput. 2016. PMID: 26613419 Free PMC article.

7

Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge.

König G, Pickard FC 4th, Huang J, Simmonett AC, Tofoleanu F, Lee J, Dral PO, Prasad S, Jones M, Shao Y, Thiel W, Brooks BR. König G, et al. Among authors: simmonett ac. J Comput Aided Mol Des. 2016 Nov;30(11):989-1006. doi: 10.1007/s10822-016-9936-x. Epub 2016 Aug 30. J Comput Aided Mol Des. 2016. PMID: 27577746

8

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK _a corrections.

Pickard FC 4th, König G, Tofoleanu F, Lee J, Simmonett AC, Shao Y, Ponder JW, Brooks BR. Pickard FC 4th, et al. Among authors: simmonett ac. J Comput Aided Mol Des. 2016 Nov;30(11):1087-1100. doi: 10.1007/s10822-016-9955-7. Epub 2016 Sep 19. J Comput Aided Mol Des. 2016. PMID: 27646286

9

An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations.

Pickard FC 4th, König G, Simmonett AC, Shao Y, Brooks BR. Pickard FC 4th, et al. Among authors: simmonett ac. Bioorg Med Chem. 2016 Oct 15;24(20):4988-4997. doi: 10.1016/j.bmc.2016.08.031. Epub 2016 Aug 22. Bioorg Med Chem. 2016. PMID: 27667551 Free PMC article.

10

An empirical extrapolation scheme for efficient treatment of induced dipoles.

Simmonett AC, Pickard FC 4th, Ponder JW, Brooks BR. Simmonett AC, et al. J Chem Phys. 2016 Oct 28;145(16):164101. doi: 10.1063/1.4964866. J Chem Phys. 2016. PMID: 27802661 Free PMC article.

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