×
Guzman, Horacio V.; Tretyakov, Nikita; Kobayashi, Hideki; Fogarty, Aoife C.; Kreis, Karsten; Krajniak, Jakub; Junghans, Christoph; Kremer, Kurt; Stuehn, Torsten

ESPResSo++ 2.0: advanced methods for multiscale molecular simulation. (English) Zbl 07683956

Comput. Phys. Commun. 238, 66-76 (2019).
Summary: Molecular simulation is a scientific tool used in many fields including material science and biology. This requires constant development and enhancement of algorithms within molecular simulation software packages. Here, we present computational tools for multiscale modeling developed and implemented within the ESPResSo++ package. These include the latest applications of the adaptive resolution scheme, the hydrodynamic interactions through a lattice Boltzmann solvent coupled to particle-based molecular dynamics, the implementation of the hierarchical strategy for equilibrating long-chained polymer melts and a heterogeneous spatial domain decomposition.
The software design of ESPResSo++ has kept its highly modular C++ kernel with a Python user interface. Moreover, it has been enhanced by automatic scripts that parse configurations from other established packages, providing scientists with the ability to rapidly set up their simulations.

MSC:

82-XX Statistical mechanics, structure of matter
76-XX Fluid mechanics

Keywords:

molecular dynamics; multiscale modeling; coarse graining; soft matter; lattice Boltzmann; molecular simulations; high performance computer; computational physics

Software:

ESPResSo++; SciPy; NumPy; GitHub; Scikit; Doxygen; Gromacs; Python; PyEMMA; HDF; Boost C++ Libraries; Boost; pandas; NAMD
Cite Review PDF
Full Text: DOI arXiv

References:

[1] Kremer, K.; Müller-Plathe, F., Mol. Simul., 28, 8-9, 729-750 (2002)
[2] (Attig, N.; Binder, K.; Grubmüller, H.; Kremer, K., Computational Soft Matter: From Synthetic Polymers to Proteins. Computational Soft Matter: From Synthetic Polymers to Proteins, NIC Lecture Notes, vol. 23 (2004), Forschungszentrum Jülich)
[3] (Voth, G. A., Coarse-Graining of Condensed Phase and Biomolecular Systems (2008), CRC Press, Boca Raton, Florida)
[4] (Holm, C.; Kremer, K., Advanced Computer Simulation Approaches for Soft Matter Science I-III. Advanced Computer Simulation Approaches for Soft Matter Science I-III, Series: Advances in Polymer Science, vol. 173, 185, 221 (2005), Springer, Berlin)
[5] Peter, C.; Kremer, K., Faraday Discuss., 144, 9-24 (2005)
[6] Halverson, J. D., Comput. Phys. Comm., 184, 4, 1129 (2013)
[7] Liu, A. J., Soft Matter, 11, 2326-2332 (2015)
[8] Rapaport, D., Comput. Phys. Comm., 62, 2, 198-216 (1991)
[9] Shaw, D. E., (Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis (2009)), 1-11
[10] Guzman, H. V., Beilstein J. Nanotechnol., 8, 968-974 (2017)
[11] Mashayak, S. Y., PLoS One, 10, 7, 1-20 (2015)
[12] Potestio, R., Phys. Rev. Lett., 110, 108301 (2013)
[13] Dünweg, B.; Schiller, U. D.; Ladd, A. J.C., Phys. Rev. E, 76, 036704 (2007)
[14] Guzman, H. V.; Junghans, C.; Kremer, K.; Stuehn, T., Phys. Rev. E, 96, 053311 (2017)
[15] Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E., J. Chem. Theory Comput., 4, 435-447 (2008)
[16] Plimpton, S., J. Comput. Phys., 117 (1995) · Zbl 0830.65120
[17] Phillips, J. C., J. Comput. Chem., 26, 1781-1802 (2005)
[18] Limbach, H. J.; Arnold, A.; Mann, B. A.; Holm, C., Comput. Phys. Comm., 174(9), 707-727 (2006)
[19] Kreis, K.; Potestio, R.; Kremer, K.; Fogarty, A. C., J. Chem. Theory Comput., 12, 8, 4067-4081 (2016)
[20] de Buyl, P.; Nies, E., J. Chem. Phys., 142, 13, 134102 (2015)
[21] Krajniak, J.; Zhang, Z.; Pandiyan, S.; Nies, E.; Samaey, G., J. Comput. Chem., 39, 22, 1764-1778 (2018)
[22] Krajniak, J.; Pandiyan, S.; Nies, E.; Samaey, G., J. Chem. Theory Comput., 12, 11, 5549-5562 (2016)
[23] Krajniak, J.; Zhang, Z.; Pandiya, n. S.; Nies, E.; Samaey, G., J. Comput. Chem., 39, 11, 648-664 (2017)
[24] Praprotnik, M.; Site, L. D.; Kremer, K., Annu. Rev. Phys. Chem., 59, 545 (2008)
[25] Praprotnik, M.; Junghans, C.; Delle Site, L.; Kremer, K., Comput. Phys. Comm., 179, 51-60 (2008)
[26] Poblete, S.; Praprotnik, M.; Kremer, K.; Site, L. D., J. Chem. Phys., 132, 11, 114101 (2010)
[27] Praprotnik, M.; Poblete, S.; Kremer, K., J. Stat. Phys., 946-966 (2011) · Zbl 1231.82006
[28] Ahlrichs, P.; Dünweg, B., J. Chem. Phys., 111, 17, 8225-8239 (1999)
[29] Praprotnik, M.; Site, L. D.; Kremer, K., J. Chem. Phys., 123, 22, 224106-224114 (2005)
[30] Praprotnik, M.; Matysiak, S.; Site, L. D.; Kremer, K.; Clementi, C., J. Phys.: Condens. Matter, 19, 29, 292201 (2007)
[31] Praprotnik, M.; Matysiak, S.; Site, L. D.; Kremer, K.; Clementi, C., J. Phys.: Condens. Matter, 21, 49, 499801 (2009)
[32] Fogarty, A. C.; Potestio, R.; Kremer, K., J. Chem. Phys., 142, 19, 195101 (2015)
[33] Kreis, K.; Fogarty, A. C.; Kremer, K.; Potestio, R., Eur. Phys. J. Spec. Top., 224, 12, 2289 (2015)
[34] Kreis, K.; Potestio, R., J. Chem. Phys., 145, 4, 044104 (2016)
[35] Zavadlav, J.; Podgornik, R.; Praprotnik, M., J. Chem. Theory Comput., 11, 10, 5035 (2015)
[36] Kreis, K.; Tuckerman, M. E.; Donadio, D.; Kremer, K.; Potestio, R., J. Chem. Theory Comput., 12, 7, 3030-3039 (2016)
[37] Kreis, K.; Kremer, K.; Potestio, R.; Tuckerman, M. E., J. Chem. Phys., 147, 24, 244104 (2017)
[38] Delgado-Buscalioni, R.; Kremer, K.; Praprotnik, M., J. Chem. Phys., 128, 114110 (2008)
[39] Delgado-Buscalioni, R.; Kremer, K.; Praprotnik, M., J. Chem. Phys., 131, 24, 244107 (2009)
[40] Kreis, K.; Donadio, D.; Kremer, K.; Potestio, R., Europhys. Lett., 108, 3, 30007 (2014)
[41] Zhang, G.; Moreira, L. A.; Stuehn, T.; Daoulas, K. C.; Kremer, K., ACS Macro Lett., 3, 2, 198-203 (2014)
[42] Oliphant, T. E., A Guide to NumPy (2006), Trelgol Publishing
[43] E. Jones, T.E. Oliphant, P. Peterson, et al. SciPy: Open source scientific tools for Python, 2001-, [Online; accessed ¡today¿].
[44] Pedregosa, F.; Varoquaux, G., J. Mach. Learn. Res., 12, 2825-2830 (2011) · Zbl 1280.68189
[45] Mckinney, W., (Varoquaux, G.; van der Walt, S.; Millman, J., Proceedings of the 9th Python in Science Conference (2010)), 51-56
[46] Scherer, M. K., J. Chem. Theory Comput., 11, 5525-5542 (2015)
[47] ESPResSo++ Website, ESPResSo++, 2010-2018, http://www.espresso-pp.de.
[48] ESPResSo++ Developers, ESPResSo++ GitHub repository, 2014-2018, https://github.com/espressopp/espressopp.
[49] ESPResSo++ Developers, ESPResSo++ website, 2010-2018, http://www.espresso-pp.de/Documentation/index.html.
[50] E, W.; Engquist, B.; Huang, Z., Phys. Rev. B, 67, 092101 (2003)
[51] Roehm, D., Comput. Phys. Comm., 192, 138-147 (2015)
[52] Meier, K., Angew. Chem. Int. Ed., 52, 10, 2820-2834 (2013)
[53] Delle Site, L.; Praprotnik, M., Phys. Rep., 693, 1 (2017) · Zbl 1370.81098
[54] Praprotnik, M.; Delle Site, L.; Kremer, K., J. Chem. Phys., 123, 22, 224106 (2005)
[55] Potestio, R.; Peter, C.; Kremer, K., Entropy, 16, 8, 4199 (2014)
[56] Lambeth, B. P.; Junghans, C.; Kremer, K.; Clementi, C.; Delle Site, L., J. Chem. Phys., 133, 22, 221101 (2010)
[57] Fritsch, S.; Junghans, C.; Kremer, K., J. Chem. Theory Comput., 8, 2, 398 (2012)
[58] Mukherji, D.; van der Vegt, N. F.A.; Kremer, K.; Delle Site, L., J. Chem. Theory Comput., 8, 2, 375 (2012)
[59] Mukherji, D.; Kremer, K., Macromolecules, 46, 22, 9158 (2013)
[60] Wang, H.; Hartmann, C.; Schütte, C.; Delle Site, L., Phys. Rev. X, 3, 1, 011018 (2013)
[61] Zavadlav, J.; Melo, M. N.; Marrink, S. J.; Praprotnik, M., J. Chem. Phys., 140, 5, 054114 (2014)
[62] Peters, J. H.; Klein, R.; Delle Site, L., Phys. Rev. E, 94, 2, 023309 (2016)
[63] Sablić, J.; Praprotnik, M.; Delgado-Buscalioni, R., Soft Matter, 12, 2416-2439 (2016)
[64] Netz, P. A.; Potestio, R.; Kremer, K., J. Chem. Phys., 145, 23, 234101 (2016)
[65] Fogarty, A. C.; Potestio, R.; Kremer, K., Proteins: Struct. Funct. Bioinform., 84, 12, 1902-1913 (2016)
[66] Fiorentini, R.; Kremer, K.; Potestio, R.; Fogarty, A. C., J. Chem. Phys., 146, 24, 244113 (2017)
[67] Potestio, R., Phys. Rev. Lett., 111, 6, 060601 (2013)
[68] Español, P., J. Chem. Phys., 142, 6, 064115 (2015)
[69] Delle Site, L., Phys. Rev. E, 76, 4, 047701 (2007)
[70] Praprotnik, M.; Delle Site, L.; Kremer, K., Phys. Rev. E, 73, 6, 066701 (2006)
[71] Praprotnik, M.; Kremer, K.; Site, L. D., Phys. Rev. E, 75, 1 (2007)
[72] Praprotnik, M.; Kremer, K.; Site, L. D., J. Phys. A, 40, 15, F281-F288 (2007) · Zbl 1114.81340
[73] Poblete, S.; Praprotnik, M.; Kremer, K.; Delle Site, L., J. Chem. Phys., 132, 11, 114101 (2010)
[74] Praprotnik, M.; Poblete, S.; Delle Site, L.; Kremer, K., Phys. Rev. Lett., 107, 099801 (2011)
[75] Potestio, R.; Delle Site, L., J. Chem. Phys., 136, 5, 054101 (2012)
[76] Poma, A. B.; Site, L. D., Phys. Rev. Lett., 104, 250201 (2010)
[77] Poma, A. B.; Delle Site, L., Phys. Chem. Chem. Phys., 13, 10510 (2011)
[78] Stillinger, F. H.; Sakai, H.; Torquato, S., J. Chem. Phys., 117, 1, 288 (2002)
[79] Louis, A. A., J. Phys. Condens. Matter, 14, 40, 9187 (2002)
[80] Wang, H.; Junghans, C.; Kremer, K., Eur. Phys. J. E, 28, 2, 221 (2009)
[81] D’Adamo, G.; Pelissetto, A.; Pierleoni, C., J. Chem. Phys., 138, 23, 234107 (2013)
[82] Kirkwood, J. G., J. Chem. Phys., 3, 5, 300 (1935) · Zbl 0012.04704
[83] Fritsch, S.; Poblete, S.; Junghans, C.; Ciccotti, G.; Site, L. D.; Kremer, K., Phys. Rev. Lett., 108, 170602 (2012)
[84] Tuckerman, M. E.; Berne, B. J.; Martyna, G. J., J. Chem. Phys., 97, 3, 1990-2001 (1992)
[85] Tuckerman, M. E., Statistical Mechanics: Theory and Molecular Simulation (2010), Oxford University Press: Oxford University Press New York · Zbl 1232.82002
[86] Feynman, R.; Hibbs, A. R., Quantum Mechanics and Path Integrals (1965), McGraw-Hill: McGraw-Hill New York · Zbl 0176.54902
[87] Pérez, A.; Tuckerman, M. E.; Hjalmarson, H. P.; Von Lilienfeld, O. A., J. Am. Chem. Soc., 132, 33, 11510-11515 (2010)
[88] Li, X. Z.; Probert, M. I.J.; Alavi, A.; Michaelides, A., Phys. Rev. Lett., 104, 6, 066102 (2010)
[89] Nagata, Y.; Pool, R. E.; Backus, E. H.G.; Bonn, M., Phys. Rev. Lett., 109, 22, 226101 (2012)
[90] Pamuk, B., Phys. Rev. Lett., 108, 19, 193003 (2012)
[91] Wang, L.; Fried, S. D.; Boxer, S. G.; Markland, T. E., Proc. Natl. Acad. Sci. USA, 111, 52, 18454-18459 (2014)
[92] Benzi, R.; Succi, S.; Vergassola, M., Phys. Rep., 222, 3, 145197 (1992)
[93] Qian, Y. H.; D’Humires, D.; Lallemand, P., Europhys. Lett., 17, 6, 479 (1992) · Zbl 1116.76419
[94] Succi, S., The Lattice Boltzmann Equation for Fluid Dynamics and Beyond (2001), Clarendon Press: Clarendon Press Oxford · Zbl 0990.76001
[95] Dünweg, B.; Ladd, A. J., (Holm, C.; Kremer, K., Advanced Computer Simulation Approaches for Soft Matter Sciences III. Advanced Computer Simulation Approaches for Soft Matter Sciences III, Advances in Polymer Science, vol. 221 (2009), Springer Berlin Heidelberg), 89-166
[96] Aidun, C. K.; Clausen, J. R., Annu. Rev. Fluid Mech., 42, 1, 439472 (2010)
[97] d’Humires, D.; Ginzburg, I.; Krafczyk, M.; Lallemand, P.; Luo, L. S., Philos. Trans.: Math. Phys. Eng. Sci., 360, 1792, 437-451 (2002) · Zbl 1001.76081
[98] Tretyakov, N.; Dnweg, B., Comput. Phys. Comm., 216, 102108 (2017)
[99] de Gennes, P. G., J. Chem. Phys., 55, 2, 572-579 (1971)
[100] Doi, M.; Edwards, S., J. Chem. Soc., Faraday Transactions 2: Mol. Chem. Phys., 74, 1789-1801 (1978)
[101] Doi, M.; Edwards, S. F., The Theory of Polymer Dynamics, Vol. 73 (1988), Oxford university press
[102] Zhang, G.; Stuehn, T.; Daoulas, K. C.; Kremer, K., J. Chem. Phys., 142, 221102 (2015)
[103] Vettorel, T.; Besold, G.; Kremer, K., Soft Matter, 6, 10, 2282-2292 (2010)
[104] Auhl, R.; Everaers, R.; Grest, G. S.; Kremer, K.; Plimpton, S. J., J. Chem. Phys., 119, 24, 12718-12728 (2003)
[105] Moreira, L. A.; Zhang, G.; Müller, F.; Stuehn, T.; Kremer, K., Macromol. Theory Simul., 24, 5, 419-431 (2015)
[106] Shaw, D., J. Comput. Chem., 26, 13, 1318-1328 (2005)
[107] Kremer, K.; Grest, G. S., J. Chem. Phys., 92, 8, 5057-5086 (1990)
[108] S. Lowe, Using the Fork-and-Branch Git Workflow, 2015, (last accessed: 05.05.2018).
[109] Booch, G., Object Oriented Design: With Applications, The Benjamin/Cummings Series in Ada and Software Engineering (1991), Benjamin/Cummings Pub.
[110] R.M. Stallman, Free Software Foundation, 2016.
[111] Lattner, C., (The BSD Conference (2008)), 1-2
[112] Karlsson, B., Beyond the C++ Standard Library: An Introduction to Boost (2005), Pearson Education
[113] 2011, Doxygen: Documentation generation system.
[114] P.W. Tom, Semantic versioning v2.0.0.
[115] O. Lenz, et al. espressopp/espressopp: ESPResSo++ 2.0, 2018.
[116] Pérez, F.; Granger, B. E., Comput. Sci. Eng., 9, 3, 21-29 (2007)
[117] de Buyl, P.; Colberg, P. H.; Hoefling, F., Comput. Phys. Comm., 185, 6, 1546-1553 (2014)
[118] The HDF Group, Hierarchical Data Format, version 5, 1997-2016, http://www.hdfgroup.org/HDF5/.
[119] Hess, B.; Kutzner, C.; Van Der Spoel, D.; Lindahl, E., J. Chem. Theory Comput., 4, 3, 435 (2008)
[120] ESPResSo++ Developers, ESPResSo++ Examples repository, 2014-2018, https://github.com/espressopp/espressopp/tree/master/examples.
This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. In some cases that data have been complemented/enhanced by data from zbMATH Open. This attempts to reflect the references listed in the original paper as accurately as possible without claiming completeness or a perfect matching.