https://user.eng.umd.edu/~jbklauda/wiki/ 2026-11-11T11:42:35+00:00 https://user.eng.umd.edu/~jbklauda/wiki/ https://user.eng.umd.edu/~jbklauda/wiki/lib/tpl/dokuwiki/images/favicon.ico text/html 2022-04-23T14:22:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=1d_z_namd_potential_of_mean_force&rev=1650738146&do=diff Umbrella Sampling Method for PMF Created by Robert Allsopp This is an implementation of umbrella sampling to generate a PMF in NAMD systems this example uses distanceZ for a Z dimensional reaction coordinate. Downolad the files from here , this link has updated files for different systems to run PMF pulling or setup windows in bash vs csh for example text/html 2026-09-24T00:24:45+00:00 Anonymous (anonymous@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 2021-12-07T15:09:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=adjusting_water_level_and_mutating_residues_of_existing_simulations&rev=1638907753&do=diff Written By Robert To Adjust the water level of the simulation (Robert): * Generate a PDB of the simulation using the steps from the NAMD PMF section where the PDB of the adjusted simulation is generated. * Download and open the PDB in VMD * Use the code below and adjust the -50 and 35 to get the right water level. Less water will speed the simulation. text/html 2021-11-10T19:29:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=adjusting_water_level_mutating_residues_of_existing_simulations&rev=1636590561&do=diff Written By Robert To Adjust the water level of the simulation (Robert): * Generate a PDB of the simulation using the steps from the NAMD PMF section where the PDB of the adjusted simulation is generated. * Download and open the PDB in VMD * Use the code below and adjust the -50 and 35 to get the right water level. Less water will speed the simulation. text/html 2021-11-10T19:30:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=analysis&rev=1636590655&do=diff bilayer_simulations Bilayer Analysis Instructions Here are a list of instructions for properties you may want to compute: * Surface Area of Lipid (overall) * Equilb Test and Area Compressibility * Comp-SA (surface area of each lipid component) * SCD (chain order parameters) * EDP (electron density profiles) text/html 2026-03-04T00:09:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=asymmetric_bilayer&rev=1772600943&do=diff bilayer_simulations Asymmetric membrane builder Created by Dr. Min-Kang Hsieh Contact email: mkhsieh1027@gmail.com Update (02.15.2026): The update (asym_memb_builder_v5.tgz) reflects the corresponding modification of ion residue names in IONS, replacing the POT and CAL resnames. In Step 6, phosphorus atoms are constrained in step5_input.ref following CHARMM minimization. Using the helper file (./namd/membrane_lipid_phos_restraint.namd.str), users can modify the constraint settings as nee… text/html 2023-09-01T16:06:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=backup&rev=1693598777&do=diff sidebar Backup Data Instructions Contained in this wiki are instructions for backing your data on the Klauda Lab Backup Server. The name of this server is klauda-bkup1.umd.edu and can only be reached on computers on the UMD network. Your UMD password/userid is needed to log into this server. You'll need to logon to ZT1 first if you need to access this server outside campus without VPN. text/html 2025-10-24T09:22:14+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=bilayer_simulations&rev=1761312134&do=diff Typical Procedure for Bilayer Simulations 1. Create Bilayer 2. Membrane Simulation 3. Production Run 4. Analysis 5. Membrane Protein Analysis Non-standard Bilayer Builds 1. Membranes+Chemicals 2. PMF of chemicals (1-D) 3. Dual Bilayer+Chemical 4. Mutating a lipid 5. Asymmetric Bilayer 6. Transmembrane Helix Dimers text/html 2017-05-21T23:05:59+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=blob_bot.py&rev=1495422359&do=diff # MEMBRANE PACKING DEFECT ANALYSIS # WRITTEN FOR: PYTHON (v 2.7.8) and openCV (v 3.1.0) # USES MODULES: numpy, os, cv2 # CREATED BY: KY WILDERMUTH (05/2016) # # This script will conduct various packing defect analysis on a single leaflet of a lipid membrane. # It will produce three output files that provide the following data for each frame in the image set: # (1) "local_defect.dat" provides the total normal area of defect exposure directly below the protein, # the normal area of the prot… text/html 2017-05-21T23:04:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=blob_top.py&rev=1495422285&do=diff # MEMBRANE PACKING DEFECT ANALYSIS # WRITTEN FOR: PYTHON (v 2.7.8) and openCV (v 3.1.0) # USES MODULES: numpy, os, cv2 # CREATED BY: KY WILDERMUTH (05/2016) # # This script will conduct various packing defect analysis on a single leaflet of a lipid membrane. # It will produce three output files that provide the following data for each frame in the image set: # (1) "local_defect.dat" provides the total normal area of defect exposure directly below the protein, # the normal area of the prot… text/html 2017-12-21T20:20:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=bridges&rev=1513905601&do=diff Bridges has two partitions: pylon2 and pylon5. pylon2 is for longer storage with little space while pylon5 is temporary and for bigger files. You will do work in pylon5. Make sure to clear out pylon5 regularly as there is only 500 GB of space. Bridges has a policy of using text/html 2018-05-08T11:48:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=building_a_hydrate_lattice&rev=1525794514&do=diff (The files for the programs mentions below can be found here ) Overview To build the gas hydrate lattice, you need to obtain the coordinates of the oxygen atoms in a unit cell and use the program Avicci to insert hydrogen atoms in such a way as to minimize the overall dipole of the unit cell while abiding by the Bernal–Fowler ice rules. The program then fills the cages of hydrate slab as the the input specifies. text/html 2026-08-17T19:44:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=chain_interdigitation&rev=1787010286&do=diff Analysis Interdigitation Analysis Author: Eric Wang Please email me at ericzwang@gmail.com if something isn't clear This instruction is very similar to EDP because it relies on density profiles. I removed recentering from this analysis to save space. Add it in if you haven't done EDP. text/html 2022-09-21T09:22:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=cluster_set-up&rev=1663766546&do=diff sidebar Instructions depend on the cluster you are using. Click on the link below that is appropriate. Local Zaratan Cluster: ZT1 Details on How to run NAMD on XSEDE with Example Scripts Stampede2 Bridges Comet Rockfish Expanse Backups of DATA Data on Zaratan must be backed up. Click on the link below that describes how to back your data up. text/html 2019-01-31T10:35:57+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=comet&rev=1548948957&do=diff Here is the instructions to run NAMD on comet supercomputer: your work directory is as follows: /oasis/scratch/comet/username all the files that you need to start a simulation are: equil.scr (for equilibrating a system with membrane) dyn.csh dyn.scr last.seqno dyn-1.inp dyn-2.inp text/html 2026-09-03T09:56:24+00:00 Anonymous (anonymous@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 2016-11-16T14:28:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=contact&rev=1479324512&do=diff Lab Head Dr. Jeff Klauda : jbklauda@umd.edu Original Wiki Design Nao Rho : skdh2010@gmail.com text/html 2016-09-20T11:16:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=create_bi-layer&rev=1474384568&do=diff bilayer_simulations If you want to create a lipid bi-layer or lipid bi-layer with proteins for NAMD simulations, go to <http://www.charmm-gui.org/?doc=input/membrane>. text/html 2022-05-31T16:59:29+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=create_bilayer&rev=1654030769&do=diff bilayer_simulations Create a Bilayer If you want to create a lipid bilayer or lipid bilayer with protein for simulations, go to <http://charmm-gui.org/?doc=input/membrane.bilayer> General Rules of Thumb for Lipid Only Systems * Build bilayers based on number of lipids not size * Unless otherwise stated make sure the number of lipids is equal for each leaflet (total and individual) text/html 2017-05-21T23:07:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=defect_peptide_frequency.py&rev=1495422463&do=diff # determines the frequency of peptide # uses local_defect output from blob script and truDiff coordinates output # Written by Ky Wildermuth, 11/16. Feel free to edit. Feel free to ask questions: kywildermuth@gmail.com import pandas as pd import numpy as np import glob import re #### USER INPUT PARAMETERS ##### # define molecular interaction cutoff in Angstroms (choose large max_cutoff (ex 100) and small min_cutoff (ex -100) if don't want) max_cutoff = 20 min_cutoff = 0 # define the frame … text/html 2017-05-21T23:03:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=defect_tachyon.csh&rev=1495422197&do=diff #!/bin/csh #SBATCH -J 901_VMD # Job name #SBATCH -o 901_VMD.o%j # output and error file name (%j expands to jobID) #SBATCH -N 1 # total number of nodes #SBATCH -t 24:00:00 # run time (hh:mm:ss) #SBATCH -p scavenger # queue (partition) -- normal, development, etc. cd /lustre/kwilder/alps3/rep1/dyn1 set vmd = /lustre/home/jbklauda/vmd/vmd-1.9.2/exec/vmd $vmd -dispdev win -e defect_tachyon_scav.tcl text/html 2017-05-21T22:59:49+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=defect_tachyon_scav.tcl&rev=1495421989&do=diff # Uses VMD version 1.9.2 # Written by Ky Wildermuth (May 2016) # updated (Aug 27 2016): add protein min/max datafile for cutoff analysis. add PBC dimension datafile for granger timeseries # updated (Oct 17 2016): configured such that protein images do not include membrane elements # updated (Jan 01 2017): New wrapping command seems to work better (-centersel). # NOTES AND DIRECTIONS: # Script assumes membrane is centered at origin (z-coord) # Modify dcd and psf to be read, and home directory t… text/html 2016-08-28T15:02:52+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=delete_rename_page&rev=1472410972&do=diff Dokuwiki 1. Go to a page where you want to delete/rename. 2. Click edit page then cut the entire text. 3. Save the page blank. This will delete the page. 4. If you want to rename the file, then create page, paste text, and create new page. 5. Done :D. text/html 2023-08-14T09:02:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=dipole_potential_and_esp&rev=1692018141&do=diff Calculate electrostatic potential of a bilayer with respect to z This wiki explains how to calculate the total electrostatic potential of a bilayer with respect to position in z. The dipole potential drop can then be found by subtracting the electrostatic potential of bulk water from the potential at the center of the bilayer. (Using the scripts provided, the electrostatic potential is defined as zero at the center of the bilayer.) text/html 2021-08-31T18:53:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=distance_to_bilayer&rev=1630450404&do=diff By Robert Allsopp Downolad the files from here There are a few ways to gather the distance data. Each with different results. 1) Using VMD with weights 2) Using VMD without weights 3) Using Charmm (without weights same as VMD without weights) 4) EDP Method text/html 2016-09-25T22:14:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=dokuwiki&rev=1474856046&do=diff resource For admin 1. How to add an account for wiki. Register user For user 1. How to write a page. Write page 2. How to rename/delete a page. delete/rename page 3. How to format code. format code 4. How to put a table put table text/html 2021-08-31T18:08:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=drug_or_peptide_distance_to_bilayer&rev=1630447736&do=diff Distance to bilayer text/html 2021-06-30T09:59:44+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=dt&rev=1625061584&do=diff sidebar Listed below are instructions for setting up an account on deepthought2 (DT2) located at UMD. Instructions: Dr. Klauda will submit a request to add you as a user to our account on DT2. Once this is done, you should get a generic email from IT regarding the resource. text/html 2018-03-02T11:00:28+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=dual_bilayer_chemical&rev=1520006428&do=diff test text/html 2026-08-27T18:29:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=edp&rev=1787869777&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) text/html 2026-07-25T13:16:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=equilb_test&rev=1784999771&do=diff Get the equilibrium data (test) (main author: Yalun Yu, email: alanyu17@terpmail.umd.edu / yalun.research@gmail.com) (updates: Joshua Lucker, email: jlucker1@umd.edu) (Error handling updates: Eric Zhang, email: ezhang32@umd.edu) < Email jlucker1@umd.edu if you have any questions about this wiki page > text/html 2021-08-22T18:49:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=expanse&rev=1629672553&do=diff Here is the instructions to run NAMD on Expanse. Your work directory is as /expanse/lustre/scratch/$USER/temp_project/ Example files for equilibrium run (first-dyn.csh and first-dyn.scr) and production run (dyn.csh, dyn.scr, dyn-1.inp, and dyn-2.inp) could be found as follows: text/html 2016-09-20T20:45:40+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=extra_software&rev=1474418740&do=diff resource 1. PuTTy SSH tool in Linux command line interface. <https://terpware.umd.edu/Windows/Title/1844> 2. winSCP SSH tool in windows GUI interface. <https://terpware.umd.edu/Windows/Title/1842> 3. VMD Molecule visualization tool. <http://www.ks.uiuc.edu/Research/vmd/> text/html 2020-12-10T08:16:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=fep&rev=1607606183&do=diff Free Energy Perturbation Calculation in CHARMM Link to FEP files in DT2: /lustre/jbklauda/FEP/FEP_example.zip To run an FEP calculation, you will need: * A coordinate (.crd) file for your molecule in a vacuum, equilibrated. Call it “moleculename_gas.crd,” except with your molecule’s name in the place of “moleculename.” text/html 2016-09-25T22:18:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=format_code&rev=1474856312&do=diff resource Often time, you will need to post a code here to for share. Here is how you can do it. <code lang | title> some code </code> Here is an example. def function(){ print "hello, world!" } Here is the source line: <code python | code.py> def function(){ print "hello, world!" } </code> text/html 2026-08-03T12:43:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=gmvae_update&rev=1785775383&do=diff GMVAE Clustering of Protein Contacts (author: Drs. Min-Kang Hsieh and Mahdi Ghorbani) This is based off Dr. Ghorbani's GMVAE code available on Github. This has been updated to work with newer versions of python and Zaratan's architecture. Use on other HPC will likely need tweaking from the instructions below. text/html 2018-03-19T17:18:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=gnuplot_scripts&rev=1521494285&do=diff Multiplot templates will be placed here since they can be a pain to make 3×3 3×2 2×2 text/html 2025-10-24T09:47:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=gromacs&rev=1761313625&do=diff GROMACs Simulations This is based on taking CHARMM-GUI input files and adjusting these for use on Zaratan. 1. Create a Minimization and Equilibration File The code below provides an example setup for this. #!/bin/bash #SBATCH --job-name=eq_bilayer #SBATCH -A energybio-eng #SBATCH -t 72:00:00 #SBATCH -N 1 #SBATCH -n 32 module load gromacs/2019.4/gcc/ export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}" set -euo pipefail # ---- 6.0 Minimization ---- #srun gmx_mpi grompp -f step6.0_minimizatio… text/html 2019-03-20T12:29:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=hmmm&rev=1553099382&do=diff Distance to bilayer text/html 2026-10-11T23:01:00+00:00 Anonymous (anonymous@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 2022-11-07T08:45:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=hydrogen_bonds_for_single-component_bilayers&rev=1667828719&do=diff Analysis Brief instruction to obtain H-bond by CHARMM script for a Single Lipid Bilayer Authors: Xiaohong Zhuang and Dr. Jeffery B. Klauda This instruction is to explain the procedure to calculate the number of H-bonding in single lipid bilayer including the PBC. text/html 2022-01-12T10:17:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=interaction_energy_of_ligand_in_charmm&rev=1642000625&do=diff This is a tutorial on how to calculate the interaction energy and it is worth noting that there was help from other sources such as a template code on the Charmm source codes website by Lennart Nilsson. Begin by downloading the source files It is important to re-center the trajectory so that system is always in the center. There is a way to check if everything works by averaging together the total interaction energy, total electrostatic, and total VdW energies and seeing if the sum of the ave… text/html 2016-09-25T22:21:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=linux_guide&rev=1474856510&do=diff resource This page is for people who are not familiar with linux. 1. Permission Often, the OS will say “permission denied”, when you try to run/edit a file. Do not panic and follow this guide. chmod u+x+w filename # chmod: give permission, u: for owner, text/html 2022-11-07T08:46:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=lipid_clustering&rev=1667828808&do=diff Analysis Brief instruction to calculate lipid clusters Authors: Xiaohong Zhuang and Dr. Jeffery B. Klauda This instruction is explain the procedure to perform the clustering analysis of multiple lipid bilayers. Download Script: Download Example: Copy the script folder provided in the path above to your path. text/html 2026-08-13T22:06:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=lipid_wobble&rev=1786673175&do=diff Analysis Brief instruction to obtain lipid wobbble correlation times Authors: Xiaohong Zhuang, Viviana Monje and Dr. Jeffery B. Klauda Updated by Eric Zhang to handle any lipid type automatically This brief instruction is used to calculate the time scale of lipid wobble, which describes the lipid mobility, and by calculating the correlation time (tau) of the cross-tail vectors of glycerol phospholipids (C22-C32) or sphingolipids (C4S-C2F). This could be adjusted to any vector of interest by c… text/html 2019-03-12T11:00:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=map&rev=1552402836&do=diff ---------- Ramachandran Analysis This analysis will create a Ramachandran plot for your peptide system in any range of trajectory files you desire. All scripts necessary can be found in the following path in DT2: /lustre/tcline/rama-analysis Gathering the phi-psi data text/html 2021-06-29T09:58:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=marcc&rev=1624975122&do=diff sidebar Listed below are instructions for setting up accounts on MARCC/BlueCrab located at JHU (with co-support from UMD). Instructions: If asked to form an account on MARCC you need to request to be added as a user. Use the following link: <http://www.marcc.jhu.edu/request-access/request-an-account/> Once this is done, Dr. Klauda will need to approve this request and with a day you should have an account. text/html 2018-03-02T10:59:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=membranes_chemicals&rev=1520006370&do=diff test text/html 2025-11-19T13:28:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=membrane_protein_analysis&rev=1763576883&do=diff Protein Analysis Instructions Here are a list of instructions for properties you may want to compute: * Protein Contact Map * GMVAE Update text/html 2026-07-01T15:24:38+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=membrane_simulation&rev=1782933878&do=diff bilayer_simulations Running the first membrane simulation These are based off running on Zaratan. If running on another resource see sample inputs from Dr. Klauda or others. Once you've built the bilayer in CHARMM-GUI per Dr. Klauda's instructions you'll need to download that *tgz file to the scratch filesystem on Zaratan. This should be placed in the shared folder /scratch/zt1/project/energybio/user/username. You will need to replace the 'username' with your login. You text/html 2024-07-08T08:56:28+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=mutating_a_lipid&rev=1720443388&do=diff bilayer simulations Mutating a lipid Authors: Eric Wang & Jeff Klauda Please email me at jbklauda@umd.edu if something isn't clear Mutating a lipid means changing its chemical structure. We do this when our membrane contains a lipid which is not available by default in the CHARMM force field, but the structure is similar to an existing lipid. To mutate a lipid, you'll need to create your membrane with the pre-mutated lipids using CHARMM- text/html 2025-10-24T09:32:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=non-bilayer_simulations&rev=1761312731&do=diff Protein and FEP Simulations REST2 for enhanced sampling using solute tempering. Water Soluble Protein Equilibration and Production Run. Free Energy Perturbation (FEP) Protein Analysis Phi/psi Map Secondary structure vs time Gas Hydrate Simulations Simulating Hydrocarbon Mixtures Building a Hydrate Lattice Running Simulations using GROMACs Gromacs text/html 2019-11-18T11:54:52+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=packing_defects&rev=1574096092&do=diff Analysis Packing Defect Analysis Overview Please Cite Source: Wildermuth, K.; Monje-Galvan, V.; Warburton, L. M.; Klauda, J. B., Effect of membrane lipid packing on stable binding of the ALPS peptide. Journal of Chemical Theory and Computation 2019, 15, 1418-1429. ( text/html 2022-10-23T21:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=pairwise_2d-rdf_and_clustering&rev=1666575226&do=diff Analysis Pairwise 2D-RDF and Clustering Analysis Author: Yalun Yu (alanyu17@terpmail.umd.edu; yalun.research@gmail.com) Bug fix log: 08/24/2020: An asymmetric membrane only bug found in clustering.py (line # 757); status: code fixed and updated, example not updated. text/html 2018-06-29T14:49:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=pmf_of_chemicals_1-d&rev=1530298195&do=diff bilayer simulations PMF of Permeation for Small Molecules Author: Eric Wang Please email me at ericzwang@gmail.com if something isn't clear This procedure is used to study permeation of a small molecule through a bilayer. Conventional MD may not be satisfactory due to large energy barriers which hinder ergodicity. Therefore, we restrain the molecule at a certain plane and calculate the free energy at that plane. Many independent replicates are run to sample the full system. I use CHARMM inst… text/html 2022-09-28T17:23:51+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=production_run&rev=1664400231&do=diff bilayer_simulations Production run instructions for Zaratan Listed below are some instructions for the production run simulation on Zaratan. As we discussed, this will automatically run your simulation in chunks with each being a certain length. The files to copy (not the sub-directories) are in the following location on Zaratan to your directory with step6.1 to step6.6 namd files: text/html 2020-06-24T21:30:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=protein_contact_map&rev=1593048642&do=diff Protein Contact Map (author: Dr. Min-Kang Hsieh) This brief instruction is used to generate protein contact maps by a VMD script. The VMD script is run in Deepthought instead of VMD software. The scripts are in the DT2 path : /lustre/mhsieh/contactmap/ text/html 2025-04-03T23:43:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=psi_phi_mapping_and_alpha_beta_helix&rev=1743738201&do=diff Created by Tyler Cline Uploaded By Robert Allsopp Python Variant by Abhi Senthilkumar Download the files from here this is the source of where the method was developed You'll need to upload the phipsi.txt script. This is a tcl script used for vmd console. I have hardcoded it to register the .psf file to be text/html 2016-09-25T22:17:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=put_table&rev=1474856226&do=diff Dokuwiki This is how you put a table in! ^ head ^ head2 ^ head3 ^ | content | content | content | | content | content | content | Here is an example: carbon oxygen iron diamond rust hemoglobinpencil tree hammer text/html 2016-08-28T14:49:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=register_user&rev=1472410188&do=diff Dokuwiki 1. click Admin on upper right corner. 2. Click user manager. 3. On add-account bar, fill name, password, email, and name in. 4. For group, put user. Then create account. 5. New account is now added! text/html 2017-08-04T20:08:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=resource&rev=1501891738&do=diff sidebar Simple Linux Guide Linux guide Simple Dokuwiki Guide DokuWiki Useful Software Extra Software gnuplot Scripts gnuplot Scripts Source Code Contact text/html 2017-11-06T23:52:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=rest2&rev=1510030378&do=diff Rest2 Copy rest2 folder from the following directory into the CHARMM folder: /homes/jbklauda/sim-inputs/rest2 input/output/toppar: * Create ‘toppar’ folder and copy the toppar files within the namd directory and paste them into this new folder text/html 2021-09-02T11:33:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=rmsd&rev=1630596785&do=diff Download the script files here Use the backbone by default and change the path in the first file. open unit @U read file name "/lustre/rallsopp/glucoM4/namd/dyn"@k".dcd" Also update the location of the paths in the psfcrd.str by copying and pasting the .crd and .psf files into the psf folder, or adjusting the path. text/html 2022-08-15T13:13:39+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=rockfish&rev=1660583619&do=diff By Robert Allsopp as of 8/26/2021 The newly update (08/02/2022) scripts for running NAMD on Rockfish (by Min-Kang Hsieh) This is a bash script so it is easily transferable to other machines. There is only a cpu script for now as of 8/26/2021 Updates were made to some files here. text/html 2024-01-25T16:15:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=scd&rev=1706217356&do=diff Analysis Brief instruction to obtain order parameter (SCD) by VMD script Xiaohong Zhuang and Dr. Jeffery B. Klauda This brief instruction is used to order parameter (SCD) by VMD script. The VMD script is run on Deepthought2 instead of VMD software on your own computer. text/html 2025-11-06T07:20:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=secondary_structure_vs_time&rev=1762431632&do=diff Secondary Structure using STRIDE Update 2025: An alternate version using Python is available at the end of the page - Abhi Senthilkumar The code is adopted and changed from the following script for secondary structure calculation in VMD. <https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/> This analysis computes the secondary structure of protein residues in time for a dcd trajectory. The scripts needed can be downloaded from below. text/html 2016-09-20T11:03:38+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=sidebar&rev=1474383818&do=diff Cluster Set-up Bilayer Simulations Non-bilayer Simulations Resource text/html 2018-05-31T14:13:02+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=simulating_hydrocarbon_mixtures&rev=1527790382&do=diff (The files mention below can be found at here ) A) Generating the required files for a molecule (Example: Cyclohexane) 1. Go to <http://www.acdlabs.com/home/> and create a free account. 2. Download free version of ChemSketch. 3. Open ChemSketch. 4. Click on “Structure text/html 2016-08-29T11:36:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=source_code&rev=1472484994&do=diff sidebar You can put the source code in here! text/html 2020-07-07T17:05:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=stampede2&rev=1594155913&do=diff The instructions here assume you know the basics of running NAMD and have done it on a cluster like DT already. The details specific to Stampede2 are presented here. Stampede2 has 1T of space for each user, so clear out your data once in a while. Your working directory should look similar to this text/html 2016-11-16T14:25:02+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=start&rev=1479324302&do=diff Welcome to the Klauda Lab Wiki at UMD If you want to look around the content, go to sidebar. If you are new to the dokuwiki and how to edit, go to DokuWiki. If you want to contact the members, go to Contact. text/html 2026-10-28T15:49:18+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=surface_area_of_lipid&rev=1793216958&do=diff Analysis Overall Average SA/Lipid + Ka (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 us… text/html 2025-01-17T09:46:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=tilt_angle&rev=1737125207&do=diff Analysis Brief instruction to obtain tilt angle distribution Authors: Xiaohong Zhuang and Viviana Monje Updated: Dr. Jeff Klauda (2021) This brief instruction is used to calculate tilt angle distribution of sterols/cholestrols. The scripts that you need are in ZT1 path: text/html 2025-10-24T09:30:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=transmembrane_helix_dimers&rev=1761312630&do=diff bilayer_simulations Transmembrane Helix Dimer Build Created by Nic Kalbaugh and Prof. Jeffery Klauda Contact email: jbklauda@umd.edu These instructions are for a simple transmembrane helix dimer setup where one uses protein structure prediction to obtain helix structure. AlphaFold or RCSB structures can be used as well. text/html 2017-05-21T23:06:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=trudiff.py&rev=1495422415&do=diff # Measures distance between center of mass (COM), nearest residue, and a custom selection to the average phopshate layer of a specified binding leaflet # Measurements have sign accuracy, so the distance is negative if the peptide is below the average phosphate layer of the membrane # Measurements are accurate even if the peptide crosses the PBC boundary # Output is a single data file with a column for each measurement type time series # ASSUMPTION: membrane centered at origin (z-coord), PBC cell… text/html 2017-11-08T10:38:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=water_soluble_protein&rev=1510155486&do=diff test text/html 2016-08-29T09:45:40+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=write_page&rev=1472478340&do=diff dokuwiki 1. Go to a page where you want to link a new page. 2. Click Edit Page. 3. Go to a line where you want to put a link, write the headline for new page, then square bracket it. [[headline]] - Here is an example. You can see this by clicking edit page text/html 2023-10-03T14:42:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=zt1&rev=1696358525&do=diff sidebar Listed below are instructions for setting up an account on Zaratan (ZT1) located at UMD. Instructions: Dr. Klauda will submit a request to add you as a user to our account on ZT1. Once this is done, you should get a generic email from IT regarding the resource. text/html 2021-07-15T20:05:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://user.eng.umd.edu/~jbklauda/wiki/doku.php?id=z_potential_of_mean_force&rev=1626393912&do=diff Umbrella Sampling Method for PMF Created by Robert Allsopp This is an implementation of umbrella sampling to generate a PMF in NAMD systems this example uses distanceZ for a Z dimensional reaction coordinate. Process Summary: ---------- Setp 1: Implementing a moving Colvar (Collective Variables) to restrain the peptide, antibiotic