University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Mechanical & Materials Engineering Faculty Publications Mechanical & Materials Engineering, Department of 8-30-2017 Soſtware for Extracting Deformation Gradient and Stress from MD Simulations: Simulations using the CHARMM Force Field Mehrdad Negahban University of Nebraska-Lincoln, [email protected]Lili Zhang University of Oxford Zesheng Zhang University of Nebraska-Lincoln, [email protected]John Jasa University of Nebraska-Lincoln Antoine Jérusalem University of Oxford, [email protected]Follow this and additional works at: hp://digitalcommons.unl.edu/mechengfacpub Part of the Mechanics of Materials Commons , Nanoscience and Nanotechnology Commons , Other Engineering Science and Materials Commons , and the Other Mechanical Engineering Commons is Article is brought to you for free and open access by the Mechanical & Materials Engineering, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Mechanical & Materials Engineering Faculty Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Negahban, Mehrdad; Zhang, Lili; Zhang, Zesheng; Jasa, John; and Jérusalem, Antoine, "Soſtware for Extracting Deformation Gradient and Stress from MD Simulations: Simulations using the CHARMM Force Field" (2017). Mechanical & Materials Engineering Faculty Publications. 207. hp://digitalcommons.unl.edu/mechengfacpub/207
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University of Nebraska - LincolnDigitalCommons@University of Nebraska - LincolnMechanical & Materials Engineering FacultyPublications
Mechanical & Materials Engineering, Departmentof
8-30-2017
Software for Extracting Deformation Gradient andStress from MD Simulations: Simulations using theCHARMM Force FieldMehrdad NegahbanUniversity of Nebraska-Lincoln, [email protected]
Follow this and additional works at: http://digitalcommons.unl.edu/mechengfacpub
Part of the Mechanics of Materials Commons, Nanoscience and Nanotechnology Commons,Other Engineering Science and Materials Commons, and the Other Mechanical EngineeringCommons
This Article is brought to you for free and open access by the Mechanical & Materials Engineering, Department of at DigitalCommons@University ofNebraska - Lincoln. It has been accepted for inclusion in Mechanical & Materials Engineering Faculty Publications by an authorized administrator ofDigitalCommons@University of Nebraska - Lincoln.
Negahban, Mehrdad; Zhang, Lili; Zhang, Zesheng; Jasa, John; and Jérusalem, Antoine, "Software for Extracting Deformation Gradientand Stress from MD Simulations: Simulations using the CHARMM Force Field" (2017). Mechanical & Materials Engineering FacultyPublications. 207.http://digitalcommons.unl.edu/mechengfacpub/207
Example ........................................................................................................................................................ 6
Software files and citation ............................................................................................................................ 7
The codes for conducting these calculation, this report and the example are placed on the University of
Nebraska-Lincoln Digital Commons for free access and download under the license described above. The
theoretical development should be cited using the associated articles provided in the reference section.
The software and this document are to be cited as:
Mehrdad Negahban, Lili Zhang, Zesheng Zhang, John Jasa, Antoine Jérusalem, "Software for Extracting
Deformation Gradient and Stress from MD Simulations: Simulations using the CARMM Force Field"
UNL Digital Commons, 2017.
References
1. Zhang, L., J. Jasa, G. Gazonas, A. Jérusalem, and M. Negahban, Extracting continuum-like deformation and stress from molecular dynamics simulations. Computer Methods in Applied Mechanics and Engineering, 2015. 283: p. 1010-1031.
2. Zhang, L., Z. Zhang, J. Jasa, D. Li, R.O. Cleveland, M. Negahban, and A. Jérusalem, Molecular dynamics simulations of heterogeneous cell membranes in response to uniaxial membrane stretches at high loading rates. Scientific Reports, 2017. 7(1): p. 8316.