188 related articles for article (PubMed ID: 38338727)
1. Implementation and Validation of an OpenMM Plugin for the Deep Potential Representation of Potential Energy.
Ding Y; Huang J
Int J Mol Sci; 2024 Jan; 25(3):. PubMed ID: 38338727
[TBL] [Abstract][Full Text] [Related]
2. Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.
Harger M; Li D; Wang Z; Dalby K; Lagardère L; Piquemal JP; Ponder J; Ren P
J Comput Chem; 2017 Sep; 38(23):2047-2055. PubMed ID: 28600826
[TBL] [Abstract][Full Text] [Related]
3. Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.
Peng X; Zhang Y; Chu H; Li G
J Comput Chem; 2016 Mar; 37(6):614-22. PubMed ID: 26493154
[TBL] [Abstract][Full Text] [Related]
4. SBMOpenMM: A Builder of Structure-Based Models for OpenMM.
Floor M; Li K; Estévez-Gay M; Agulló L; Muñoz-Torres PM; Hwang JK; Osuna S; Villà-Freixa J
J Chem Inf Model; 2021 Jul; 61(7):3166-3171. PubMed ID: 34251801
[TBL] [Abstract][Full Text] [Related]
5. Gaussian Accelerated Molecular Dynamics in OpenMM.
Copeland MM; Do HN; Votapka L; Joshi K; Wang J; Amaro RE; Miao Y
J Phys Chem B; 2022 Aug; 126(31):5810-5820. PubMed ID: 35895977
[TBL] [Abstract][Full Text] [Related]
6. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials.
Eastman P; Galvelis R; Peláez RP; Abreu CRA; Farr SE; Gallicchio E; Gorenko A; Henry MM; Hu F; Huang J; Krämer A; Michel J; Mitchell JA; Pande VS; Rodrigues JP; Rodriguez-Guerra J; Simmonett AC; Singh S; Swails J; Turner P; Wang Y; Zhang I; Chodera JD; De Fabritiis G; Markland TE
J Phys Chem B; 2024 Jan; 128(1):109-116. PubMed ID: 38154096
[TBL] [Abstract][Full Text] [Related]
7. Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program.
Wieder M; Fleck M; Braunsfeld B; Boresch S
J Comput Chem; 2022 Jun; 43(17):1151-1160. PubMed ID: 35485139
[TBL] [Abstract][Full Text] [Related]
8. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.
Lee J; Cheng X; Swails JM; Yeom MS; Eastman PK; Lemkul JA; Wei S; Buckner J; Jeong JC; Qi Y; Jo S; Pande VS; Case DA; Brooks CL; MacKerell AD; Klauda JB; Im W
J Chem Theory Comput; 2016 Jan; 12(1):405-13. PubMed ID: 26631602
[TBL] [Abstract][Full Text] [Related]
9. SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine.
Votapka LW; Stokely AM; Ojha AA; Amaro RE
J Chem Inf Model; 2022 Jul; 62(13):3253-3262. PubMed ID: 35759413
[TBL] [Abstract][Full Text] [Related]
10. An implementation of the Martini coarse-grained force field in OpenMM.
MacCallum JL; Hu S; Lenz S; Souza PCT; Corradi V; Tieleman DP
Biophys J; 2023 Jul; 122(14):2864-2870. PubMed ID: 37050876
[TBL] [Abstract][Full Text] [Related]
11. Alchemical Transfer Approach to Absolute Binding Free Energy Estimation.
Wu JZ; Azimi S; Khuttan S; Deng N; Gallicchio E
J Chem Theory Comput; 2021 Jun; 17(6):3309-3319. PubMed ID: 33983730
[TBL] [Abstract][Full Text] [Related]
12. Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility.
Wade AD; Bhati AP; Wan S; Coveney PV
J Chem Theory Comput; 2022 Jun; 18(6):3972-3987. PubMed ID: 35609233
[TBL] [Abstract][Full Text] [Related]
13. Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations.
Ben-Shalom IY; Lin Z; Radak BK; Lin C; Sherman W; Gilson MK
J Chem Theory Comput; 2020 Dec; 16(12):7883-7894. PubMed ID: 33206520
[TBL] [Abstract][Full Text] [Related]
14. py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD.
Barhaghi MS; Crawford B; Schwing G; Hardy DJ; Stone JE; Schwiebert L; Potoff J; Tajkhorshid E
J Chem Theory Comput; 2022 Aug; 18(8):4983-4994. PubMed ID: 35621307
[TBL] [Abstract][Full Text] [Related]
15. Leveraging the sampling efficiency of RE-EDS in OpenMM using a shifted reaction-field with an atom-based cutoff.
Rieder SR; Ries B; Kubincová A; Champion C; Barros EP; Hünenberger PH; Riniker S
J Chem Phys; 2022 Sep; 157(10):104117. PubMed ID: 36109239
[TBL] [Abstract][Full Text] [Related]
16. Prediction of octanol-water partition coefficients for the SAMPL6-[Formula: see text] molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields.
Fan S; Iorga BI; Beckstein O
J Comput Aided Mol Des; 2020 May; 34(5):543-560. PubMed ID: 31960254
[TBL] [Abstract][Full Text] [Related]
17. Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics.
Hata H; Nishiyama M; Kitao A
Biochim Biophys Acta Gen Subj; 2020 Feb; 1864(2):129395. PubMed ID: 31302180
[TBL] [Abstract][Full Text] [Related]
18. Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks.
Huang J; Lemkul JA; Eastman PK; MacKerell AD
J Comput Chem; 2018 Aug; 39(21):1682-1689. PubMed ID: 29727037
[TBL] [Abstract][Full Text] [Related]
19. grand: A Python Module for Grand Canonical Water Sampling in OpenMM.
Samways ML; Bruce Macdonald HE; Essex JW
J Chem Inf Model; 2020 Oct; 60(10):4436-4441. PubMed ID: 32835483
[TBL] [Abstract][Full Text] [Related]
20. The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.
Rizzi A; Jensen T; Slochower DR; Aldeghi M; Gapsys V; Ntekoumes D; Bosisio S; Papadourakis M; Henriksen NM; de Groot BL; Cournia Z; Dickson A; Michel J; Gilson MK; Shirts MR; Mobley DL; Chodera JD
J Comput Aided Mol Des; 2020 May; 34(5):601-633. PubMed ID: 31984465
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]