P<FONT SIZE='-2'>ACKMOL</FONT>: A package for building initial configurations for molecular dynamics simulations Export

@article{packmol, abstract = {Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules must keep safe pairwise distances. Obtaining such a molecular arrangement can be considered a packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules must be greater than some specified tolerance. We have developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straightforward. In addition, different atoms belonging to the same molecule may also be restricted to different spatial regions, in such a way that more ordered molecular arrangements can be built, as micelles, lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies from a few seconds to a few minutes in a personal computer. The input files are simple and currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and can be downloaded from . {\copyright} 2009 Wiley Periodicals, Inc. J Comput Chem, 2009}, address = {Department of Physical Chemistry, IQ-UNICAMP, University of Campinas, Brazil; Department of Computer Science IME-USP, University of S\~{a}o Paulo, Rua do Mat\~{a}o 1010, Cidade Universit\'{a}ria, 05508-090 S\~{a}o Paulo SP, Brazil; Department of Applied Mathematics, IMECC-UNICAMP, University of Campinas, CP 6065, 13081-970 Campinas SP, Brazil}, author = {Mart\'{\i}nez, L. and Andrade, R. and Birgin, E. G. and Mart\'{\i}nez, J. M.}, citeulike-article-id = {4085229}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/jcc.21224}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19229944}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19229944}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/122210103/ABSTRACT}, doi = {10.1002/jcc.21224}, issn = {1096-987X}, journal = {Journal of Computational Chemistry}, keywords = {molecular\_dynamics, packmol, paper1}, number = {13}, pages = {2157--2164}, posted-at = {2009-10-18 19:01:35}, priority = {2}, title = {P<FONT SIZE='-2'>ACKMOL</FONT>: A package for building initial configurations for molecular dynamics simulations}, url = {http://dx.doi.org/10.1002/jcc.21224}, volume = {30}, year = {2009} }

TY - JOUR ID - packmol L3 - citeulike-article-id:4085229 N2 - Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules must keep safe pairwise distances. Obtaining such a molecular arrangement can be considered a packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules must be greater than some specified tolerance. We have developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straightforward. In addition, different atoms belonging to the same molecule may also be restricted to different spatial regions, in such a way that more ordered molecular arrangements can be built, as micelles, lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies from a few seconds to a few minutes in a personal computer. The input files are simple and currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and can be downloaded from . © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 IS - 13 JF - Journal of Computational Chemistry SN - 1096-987X AD - Department of Physical Chemistry, IQ-UNICAMP, University of Campinas, Brazil; Department of Computer Science IME-USP, University of São Paulo, Rua do Matão 1010, Cidade Universitária, 05508-090 São Paulo SP, Brazil; Department of Applied Mathematics, IMECC-UNICAMP, University of Campinas, CP 6065, 13081-970 Campinas SP, Brazil EP - 2164 TI - P<FONT SIZE='-2'>ACKMOL</FONT>: A package for building initial configurations for molecular dynamics simulations VL - 30 SP - 2157 KW - molecular_dynamics KW - packmol KW - paper1 AU - Martínez, L AU - Andrade, R AU - Birgin, EG AU - Martínez, JM PY - 2009/// UR - http://dx.doi.org/10.1002/jcc.21224 ER -