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GCMC/BD Ion Simulator
This module helps users generate a series of input files necessary for ion transport GCMC/BD simulation.
Source codes (compile with g77) and user manual (PB/PNP and GCMC/BD) can be downloaded here: Please note that
  • The OPM PDB does not contain "TER" between ATOM and HETATM, so that CHARMM-GUI often fails to recognize ligand molecules. In such case, the user should manually insert "TER" in appropriate places.
References for GCMC/BD Ion Simulator:

S. Jo, T. Kim, V.G. Iyer, and W. Im (2008)
CHARMM-GUI: A Web-based Graphical User Interface for CHARMM. J. Comput. Chem. 29:1859-1865

K. I. Lee, S. Jo, H. Rui, B. Egwolf, B. Roux, and W. Im
Web-based Interface for Brownian Dynamics Simulation of Ion Channels and Its Applications to beta-barrel pores J. Comput. Chem. 33:331-339
Download PDB File: Download Source:

Upload PDB File:
PDB Format: PDB PDBx/mmCIF CHARMM

References for the GCMC/BD Ion Channel Simulation Method:

W. Im, S. Seefeld, and B. Roux (2000)
A Grand Canonical Monte Carlo-Brownian Dynamics Algorithm for Simulating Ion Channels Biophys. J. 79:788-801


W. Im and B. Roux (2002)
Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory J. Mol. Biol., 322:851-869

Next Step:
Select Model/Chain



A brief explanation of each step:
  • STEP1: Read protein coordinates
    The user can download the coordinates from RCSB (PDB website) or OPM (http://opm.phar.umich.edu). OPM provides pre-oriented protein coordiantes with respect to the membrane normal. The user can upload the PDB (or CHARMM) format coordinates from the user's local machine, once you properly orient the protein in membranes.

  • STEP2: Orient the protein
    If the PDB coordinates from RCSB, it is necessary to properly orient the protein with respect to membranes. There are two options for doing this. It is the step in which the cross-section area of the protein along the Z-axis is calculated and displayed. The maximum top (10 Å < Z < 20 Å) and bottom (-20 Å < Z < -10 Å) areas are used to determine the system size in XY. Pore water will be generated and the volume of the pore water will be included when calculating the system size. Maximum pore radius will be taken along the Z-axis (-15 Å < Z < 15 Å).

  • STEP3: Input system size, PB Option, and GCMC/BD Options
    Users can define the system size and grid spacing to a specific value and specify PB options (ion type, dielectric constants, transmembrane potential, membrane thickness, pore radius, etc) and GCMC/BD options (buffer length, diffusion profile, simulation time parameters, etc). Charge map and protein atom radii profiles (PB and Stern) are also generated from CHARMM.

    (STEP4 and STEP5 should be run at user's machine.)

  • STEP4: Generate input files for ion accessibility map, PB potential map and reaction field parameters
    Based on the system size, charge map, and PB and Stern radii profile for protein, this step builds input files for (1) steric potential, (2) PB electrostatic potential, and (3) reaction field parameters.

  • STEP5: Generate input files for GCMC/BD main run
    This step generates an input file for GCMC/BD main runs.