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Publication search results
found 19 matches
- 2020
- Mahzad Khoshlessan, Ioannis Paraskevakos, Geoffrey C. Fox, Shantenu Jha, Oliver Beckstein
:
Parallel performance of molecular dynamics trajectory analysis. Concurr. Comput. Pract. Exp. 32(19) (2020) - Yusuke Ootani
, Aya Satoh, Yu Harabuchi, Tetsuya Taketsugu
:
Trajectory on-the-fly molecular dynamics approach to tunneling splitting in the electronic excited state: A case of tropolone. J. Comput. Chem. 41(16): 1549-1556 (2020) - Linfeng Ye, Chao Xu, Feng Long Gu
, Chaoyuan Zhu
:
Functional and Basis Set Dependence for Time-Dependent Density Functional Theory Trajectory Surface Hopping Molecular Dynamics: Cis-Azobenzene Photoisomerization. J. Comput. Chem. 41(7): 635-645 (2020) - 2019
- Mahzad Khoshlessan, Ioannis Paraskevakos, Geoffrey C. Fox, Shantenu Jha, Oliver Beckstein:
Parallel Performance of Molecular Dynamics Trajectory Analysis. CoRR abs/1907.00097 (2019) - 2018
- Mauricio Carrillo-Tripp
, Leonardo Alvarez-Rivera, Omar Israel Lara-Ramírez, Francisco Javier Becerra-Toledo, Adan Vega-Ramírez, Emmanuel Quijas-Valades, Eduardo González-Zavala, Julio Cesar González-Vázquez, Javier García-Vieyra, Nelly Beatriz Santoyo-Rivera, Sergio Víctor Chapa Vergara, Amilcar Meneses Viveros
:
HTMoL: full-stack solution for remote access, visualization, and analysis of molecular dynamics trajectory data. J. Comput. Aided Mol. Des. 32(8): 869-876 (2018) - Daniel R. Roe
, Thomas E. Cheatham III:
Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data. J. Comput. Chem. 39(25): 2110-2117 (2018) - 2017
- Mauricio Carrillo-Tripp, Leonardo Alvarez-Rivera, Omar Israel Lara-Ramírez, Francisco Javier Becerra-Toledo, Adan Vega-Ramírez, Emmanuel Quijas-Valades, Eduardo González-Zavala, Julio Cesar González-Vázquez, Javier García-Vieyra, Nelly Beatriz Santoyo-Rivera, Amilcar Meneses Viveros, Sergio Víctor Chapa Vergara:
HTMoL: full-stack solution for remote access, visualization, and analysis of Molecular Dynamics trajectory data. CoRR abs/1711.08078 (2017) - 2014
- Samuel Schlachter, Stephen Herbein
, Shuching Ou, Jeremy S. Logan, Sandeep Patel, Michela Taufer
:
Pursuing Coordinated Trajectory Progression and Efficient Resource Utilization of GPU-Enabled Molecular Dynamics Simulations. IEEE Des. Test 31(1): 40-50 (2014) - Lei Wang, James W. Mazzuca, Sophya Garashchuk
, Jacek Jakowski
:
The hybrid Quantum Trajectory/Electronic Structure DFTB-based approach to Molecular Dynamics. XSEDE 2014: 24:1-24:8 - 2013
- Alexander V. Popov, Yury N. Vorobjev, Dmitry O. Zharkov:
MDTRA: A molecular dynamics trajectory analyzer with a graphical user interface. J. Comput. Chem. 34(4): 319-325 (2013) - 2012
- Patrick Marais, Julian Kenwood, Keegan Carruthers Smith, Michelle Kuttel
, James E. Gain:
Efficient compression of molecular dynamics trajectory files. J. Comput. Chem. 33(27): 2131-2141 (2012) - Yi-Ming Cheng, Srinivasa Murthy Gopal, Sean M. Law, Michael Feig:
Molecular Dynamics Trajectory Compression with a Coarse-Grained Model. IEEE ACM Trans. Comput. Biol. Bioinform. 9(2): 476-486 (2012) - 2011
- Ioannis G. Tsoulos, Athanassios Stavrakoudis
:
Eucb: A C++ program for molecular dynamics trajectory analysis. Comput. Phys. Commun. 182(3): 834-841 (2011) - Jinzen Ikebe
, Koji Umezawa, Narutoshi Kamiya, Takanori Sugihara, Yasushige Yonezawa, Yu Takano
, Haruki Nakamura, Junichi Higo:
Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water. J. Comput. Chem. 32(7): 1286-1297 (2011) - 2008
- Ales Krenek, Martin Petrek, Jan Kmunícek, Jiri Filipovic, Zdenek Sustr, Frantisek Dvorák, Jirí Sitera, Jiri Wiesner, Ludek Matyska
:
Multiple Ligand Trajectory Docking Study - Semiautomatic Analysis of Molecular Dynamics Simulations using EGEE gLite Services. PDP 2008: 447-454 - 2006
- Yan Li:
Bayesian Model Based Clustering Analysis: Application to a Molecular Dynamics Trajectory of the HIV-1 Integrase Catalytic Core. J. Chem. Inf. Model. 46(4): 1742-1750 (2006) - 2000
- Jacques Gabarro-Arpa, Roger Revilla
:
Clustering of a Molecular Dynamics Trajectory with a Hamming Distance. Comput. Chem. 24(6): 693-698 (2000) - 1999
- Michael Feig, Matin Abdullah, S. Lennart Johnsson, B. Montgomery Pettitt:
Large scale distributed data repository: design of a molecular dynamics trajectory database. Future Gener. Comput. Syst. 16(1): 101-110 (1999) - Ying-Chieh Sun, Shu-Fen Yang, I-Lung Hwang, Tzu-Hsien Wu:
A 500-ps molecular dynamics simulation trajectory of cardiotoxin II from Taiwan cobra venom in solution: Correlation with NMR and X-ray crystallography data. J. Comput. Chem. 20(5): 546-562 (1999)
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