{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T06:02:37Z","timestamp":1778911357618,"version":"3.51.4"},"reference-count":33,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2004,9,7]],"date-time":"2004-09-07T00:00:00Z","timestamp":1094515200000},"content-version":"vor","delay-in-days":3721,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[1994,7]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>New atom\u2010 and group\u2010based spherical\u2010cutoff methods have been developed for the treatment of nonbonded interactions in molecular dynamics (MD) simulation. A new atom\u2010based method, force switching, leaves short\u2010range forces unaltered by adding a constant to the potential energy, switching forces smoothly to zero over a specified range. A simple improvement to group\u2010based cutoffs is presented: Switched group\u2010shifting shifts the group\u2013group potential energy by a constant before being switched smoothly to zero. Also introduced are generalizations of atom\u2010based force shifting, which adds a constant to the Coulomb force between two charges. These new approaches are compared to existing methods by evaluating the energy of a model hydrogen\u2010bonding system consisting of two <jats:italic>N<\/jats:italic>\u2010methyl acetamide molecules and by full MD simulation. Thirty\u2010five 150 ps simulations of carboxymyoglobin (MbCO) hydrated by 350 water molecules indicate that the new methods and atom\u2010based shifting are each able to approximate no\u2010cutoff results when a cutoff at or beyond 12 \u00c5 is used. However, atom\u2010based potential\u2010energy switching and truncation unacceptably contaminate group\u2013group electrostatic interactions. Group\u2010based potential truncation should not be used in the presence of explicit water or other mobile electrostatic dipoles because energy is not a state function with this method, resulting in severe heating (about 4 K\/ps in the simulations of hydrated MbCO). The distance\u2010dependent dielectric (\u03f5 \u221d\ufe01 <jats:italic>r<\/jats:italic>) is found to alter the temperature dependence of protein dynamics, suppressing anharmonic motion at high temperatures. Force switching and force shifting are the best atom\u2010based spherical cutoffs, whereas switched group\u2010shifting is the preferred group\u2010based method. To achieve realistic simulations, increasing the cutoff distance from 7.5 to 12 \u00c5 or beyond is much more important than the differences among the three best cutoff methods. \u00a9 1994 by John Wiley &amp; Sons, Inc.<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"#n1\"\/><jats:fn><jats:p>This article is a US Government work and, as such, is in the public domain in the United States of America.<\/jats:p><\/jats:fn>\n<\/jats:p>","DOI":"10.1002\/jcc.540150702","type":"journal-article","created":{"date-parts":[[2005,1,2]],"date-time":"2005-01-02T01:05:38Z","timestamp":1104627938000},"page":"667-683","source":"Crossref","is-referenced-by-count":1090,"title":["New spherical\u2010cutoff methods for long\u2010range forces in macromolecular simulation"],"prefix":"10.1002","volume":"15","author":[{"given":"Peter J.","family":"Steinbach","sequence":"first","affiliation":[]},{"given":"Bernard R.","family":"Brooks","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2004,9,7]]},"reference":[{"key":"e_1_2_1_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(91)80181-S"},{"key":"e_1_2_1_3_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.449621"},{"key":"e_1_2_1_4_2","doi-asserted-by":"publisher","DOI":"10.1021\/j100283a017"},{"key":"e_1_2_1_5_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.452636"},{"key":"e_1_2_1_6_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.340060104"},{"key":"e_1_2_1_7_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540111009"},{"key":"e_1_2_1_8_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi00140a022"},{"key":"e_1_2_1_9_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540140304"},{"key":"e_1_2_1_10_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540140306"},{"key":"e_1_2_1_11_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.90.19.9135"},{"key":"e_1_2_1_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/0009-2614(92)90053-P"},{"key":"e_1_2_1_13_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540040211"},{"key":"e_1_2_1_14_2","unstructured":"Polygen Corporation Parameter file for CHARMm version 20 Copyright1986 released August1988."},{"key":"e_1_2_1_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/0009-2614(88)80404-4"},{"key":"e_1_2_1_16_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.1676585"},{"key":"e_1_2_1_17_2","doi-asserted-by":"publisher","DOI":"10.1080\/00268977900101751"},{"key":"e_1_2_1_18_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.448118"},{"key":"e_1_2_1_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(91)82292-5"},{"key":"e_1_2_1_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0065-3233(08)60197-7"},{"key":"e_1_2_1_21_2","doi-asserted-by":"publisher","DOI":"10.1080\/08927028808080956"},{"key":"e_1_2_1_22_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.461272"},{"key":"e_1_2_1_23_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.87.4.1601"},{"key":"e_1_2_1_24_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80196-2"},{"key":"e_1_2_1_25_2","volume-title":"Computer Simulation of Liquids","author":"Allen M. 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