Paper Citing NAMD - Abstract
Nakamura, Takenobu; Kawamoto, Shuhei; Shinoda, Wataru
Precise calculation of the local pressure tensor in Cartesian and spherical coordinates in LAMMPS
COMPUTER PHYSICS COMMUNICATIONS, 190:120-128, MAY 2015
An accurate and efficient algorithm for calculating the 3D pressure field has been developed and implemented in the open-source molecular dynamics package, LAMMPS. Additionally, an algorithm to compute the pressure profile along the radial direction in spherical coordinates has also been implemented. The latter is particularly useful for systems showing a spherical symmetry such as micelles and vesicles. These methods yield precise pressure fields based on the Irving-Kirkwood contour integration and are particularly useful for biomolecular force fields. The present methods are applied to several systems including a buckled membrane and a vesicle. Program summary Program title: Compute stress spatial Catalogue identifier: AEVH_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEVH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 7799 No. of bytes in distributed program, including test data, etc.: 149739 Distribution format: tar.gz Programming language: C++. Computer: All. Operating system: All. Supplementary material: The input and expected output for the examples given in the manuscript can be downloaded here. Classification: 7.7. Nature of problem: A precise calculation of the pressure (stress) field requires the implementation of the contour integration [2] for each pair in the cluster potentials. Solution method: We have implemented the method for calculating the local-volume average of the pressure field expressed by a contour integration with a delta function for the given molecular configuration obtained by molecular dynamics simulation [3]. Restrictions: Because the definition of pressure field is based on the contour integration, the long-range interactions represented as Ewald summation are not included. In addition, the potential represented as a combination of pair and angle potential, such as Tersoff and Stillinger-Weber potential, and the interaction as a geometric constraint (shake, rigid body, etc.) are not available for current version. Running time: The examples provided take between 3 and 6 min each to run. References: [1] S. Plimpton, Fast parallel algorithms for short-range molecular dynamics, J. Comput. Phys. 117 (1995) 1-19. [2] P. Schofield and J.R. Henderson, Proc. R. Soc. Loud. A. 379 (1982) 231. [3] T. Nakamura, W. Shinoda, and T. Ikeshoji, J. Chem. Phys. 135 (2011) 094106. (C) 2014 Elsevier B.V. All rights reserved.
