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Implementation of magnetic field force in molecular dynamics algorithm: NAMD source code version 2.12

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Abstract

The external fields, such as the magnetic force, have made advances in many industrial and biotechnology applications during the past century, although the changes in the structure of materials under the impact of the electromagnetic fields have not entirely been clear yet. The molecular simulation technique by providing extensive data from the configuration and orientations of the atoms is becoming the effective useful tool for scientists in a wide range of research areas. This paper presents an extended velocity Verlet algorithm inside the Nanoscale Molecular Dynamics (NAMD) package that enhances the NAMD features with the capability to compute the magnetic field force. We described how this novel feature has been implemented inside the package. Moreover, the results are reported for the rotation of a charged particle, and the thermo-physical properties of water in the presence of a magnetic field confirming how this developed NAMD source code provides accurate measurements compared with other available data.

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Abbreviations

B :

magnetic field \( 1\ \mathrm{T}=1\ \frac{\mathrm{kg}}{\mathrm{Amp}.{\mathrm{s}}^2}=1\frac{\mathrm{V}.\mathrm{s}}{{\mathrm{m}}^2} \)=1 \( \frac{\mathrm{kg}}{\mathrm{s}.\mathrm{C}} \)

R :

coordinate \( 1\ \mathrm{m}=1\times {10}^{10}\overset{{}^{\circ}}{\mathrm{A}} \)

∆t :

time step 1 s = 1 × 1012ps

V :

velocity \( \left[\frac{\overset{{}^{\circ}}{\mathrm{A}}}{\mathrm{pS}}\right] \)

E :

energy 1 eV = 1.602 × 10−19 J

F :

force \( 69.48\ pN=1\ \frac{\mathrm{kcal}}{\mathrm{mol}.\overset{{}^{\circ}}{\mathrm{A}}} \)

M :

mass 1 Da = 1.66 × 10−27kg

Q :

charge 1 [e] = 1.6 × 10−19 C

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Authors and Affiliations

  1. Mechanical Engineering Department, University of Tabriz, Tabriz, East Azerbaijan, 5166616471, Iran

    Kosar Khajeh & Habib Aminfar

  2. Research into Artifacts, Center for Engineering, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8568, Japan

    Yoshihiro Masuda

  3. Department of System Innovation, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan

    Yoshihiro Masuda

  4. Faculty of Chemical and Petroleum Engineering, University of Tabriz, Tabriz, Iran

    Mousa Mohammadpourfard

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  1. Kosar Khajeh
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Correspondence to Habib Aminfar.

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Khajeh, K., Aminfar, H., Masuda, Y. et al. Implementation of magnetic field force in molecular dynamics algorithm: NAMD source code version 2.12. J Mol Model 26, 106 (2020). https://doi.org/10.1007/s00894-020-4349-0

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