Hydrophobic Gating with Gromacs 3

Reference: Oliver Beckstein, Philip C. Biggin, and Mark S. P. Sansom; A Hydrophobic Gating Mechanism for Nanopores, The Journal of Physical Chemistry B; 2001; 105(51); 12902-12905. [abstract]


  1. Unpack input files
  2. Locations and Directory-naming convention
    1. general
    2. System specific
  3. Files to be modified
  4. Running a simulation

I generated input files for different pore radii from 3.5 to 10 A. This includes the pdb for the solvated system.

I am using (GNU) Makefiles to do most of the work so I also included the appropriate Makefiles. I describe what to change below (section 2) so you might be able to use them as well. In any case, you can have a look at them to find out how to run things manually.

All input files are in the tar file hygate.tar.bz2 (or hygate.tar.gz).