https://user.eng.umd.edu/~jbklauda/wiki/ 2026-10-16T15:36:25+00:00 https://user.eng.umd.edu/~jbklauda/wiki/ https://user.eng.umd.edu/~jbklauda/wiki/lib/tpl/dokuwiki/images/favicon.ico text/html 2026-10-11T23:01:00+00:00 edit (edit@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=hydrogen_bonds_for_multi-component_bilayers&rev=1791774060&do=diff Analysis Brief instructions to obtain H-bond by CHARMM script for a Multi Lipid Bilayer Original Authors: Xiaohong Zhuang and Dr. Jeffery B. Klauda Refactored by Eric Zhang (2026) to handle any membrane system This instruction explains the procedure for calculating the number of H-bonds in a multiple-lipid bilayer. For the H-bond of a single lipid system, you may use the instruction: text/html 2026-10-11T22:58:55+00:00 edit (edit@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?image=hb_asym_lipids_v2.tar.gz&ns=&rev=1791773935&tab_details=history&mediado=diff&do=media text/html 2026-09-24T00:24:45+00:00 edit (edit@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=2d_rdfs&rev=1790223885&do=diff Analysis Brief instructions to obtain 2D radial distribution function (RDF) Authors: Xiaohong Zhuang, Viviana Monje, Dr. Jeffery B. Klauda Refactored by Eric Zhang (2026): handles any membrane system These are the brief instructions to calculate the radial distribution function (RDF), also known as a pair correlation function. New users should use the modern Python scripts. they have been backtested and validated against the legacy scripts, and run 95% faster. It's also easier to use. text/html 2026-09-24T00:20:52+00:00 edit (edit@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?image=2d-rdf-asym.tar.gz&ns=&rev=1790223652&tab_details=history&mediado=diff&do=media text/html 2026-09-20T00:36:53+00:00 edit (edit@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=surface_area_of_lipid&rev=1789879013&do=diff Analysis Overall Average SA/Lipid (authors: Xiaohong Zhuang & Jeffery Klauda) Refactored by Eric Zhang (2026) Introduction This simple analysis is used to estimate the overall average surface area (SA) per lipid. If you are analyzing a single component membrane then this is equivalent to the component's SA/lipid. Otherwise, this is the average of all lipids. UPDATE: We highly recommend using the modern Python scripts for analyses (instructions listed at the very bottom). Also, those using t… text/html 2026-09-20T00:18:28+00:00 edit (edit@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?image=area_1_lipid_v2.tar.gz&ns=&rev=1789877908&tab_details=history&mediado=diff&do=media text/html 2026-09-03T09:56:24+00:00 edit (edit@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=comp-sa&rev=1788443784&do=diff Analysis Multi-lipid SA Average Instruction to obtain surface area per lipid of multicomponent system Original Authors: Xiaohong Zhuang and Viviana Monje Updated Authors: Yalun Yu and Jeffery Klauda Updated rtfpsf folder: Joshua Lucker Completely refactored, supports any membrane: Eric Zhang text/html 2026-09-02T23:57:39+00:00 edit (edit@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?image=area_asym_lipids.tar.gz&ns=&rev=1788407859&tab_details=history&mediado=diff&do=media text/html 2026-08-30T10:48:47+00:00 edit (edit@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?image=edp_asym_lipids.tar.gz&ns=&rev=1788101327&tab_details=history&mediado=diff&do=media text/html 2026-08-26T15:15:37+00:00 edit (edit@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?image=sample_rdf_plots.png&ns=&rev=1787771737&tab_details=history&mediado=diff&do=media <img src="https://user.eng.umd.edu/~jbklauda/wiki/lib/exe/fetch.php?w=378&h=500&t=1787771737&amp;tok=d86f14&amp;media=sample_rdf_plots.png" alt="sample_rdf_plots.png" /> text/html 2026-08-25T15:32:35+00:00 edit (edit@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?image=new_interdig_formulas.png&ns=&rev=1787686355&tab_details=history&mediado=diff&do=media <img src="https://user.eng.umd.edu/~jbklauda/wiki/lib/exe/fetch.php?w=316&h=500&t=1787686355&amp;tok=32d732&amp;media=new_interdig_formulas.png" alt="new_interdig_formulas.png" /> text/html 2026-08-25T15:20:31+00:00 edit (edit@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=edp&rev=1787685631&do=diff Analysis Brief Instruction to calculate electron density profile of multi-component lipids Author: Xiaohong Zhuang Updated (2021): Dr. Jeffery Klauda Updated (2021): Robert Allsopp (Combining the .sim and renaming atoms) Updated (2023): Abhi Senthilkumar (Python scripts to automatically rename atoms and combine .sim files into xlsx)