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).

[ICO]NameLast modifiedSizeDescription

[PARENTDIR]Parent Directory  -  
[   ]hygate.tar.bz22006-01-10 12:08 863K 
[TXT]Readme.html2012-01-02 19:52 5.3K 
[   ]Readme2006-01-10 12:08 4.5K 
[TXT]README.html2012-01-02 19:52 4.5K 
[TXT]HEADER.html2012-01-02 19:52 1.7K 

0 Unpack input files

Download tar archive hygate.tar.bz2 (see below). Unpack with
  tar -jxvf hygate.tar.bz2
  cd HyGate
(or tar -zxvf hygate.tar.gz)

1 Locations and Directory-naming convention

1.1 General

You need mth.itp (defines the CH4 pseudoatoms in the pore) and lay.itp (the pseudoatoms in the membrane mimetic slab). Put them in a directory of your choice, e.g. the gromacs topology directory. Or put it somewhere else and add the directory to the include list of the mdp files (see 1.2).

killwater.pl is a script which removes waters between z1 and z2; it is needed to generate input for systems with an initially empty cavity. If required it should be in the shell's search path.

vdwradii.dat is the standard van der Waals radii data file plus CH4 (r=0.195nm). It is used for the generation of the pdb files and is referenced as VDWDAT_SRC in the Makefile. You probably don't need it.

1.2 System specific

The setup files live in directories whose pathname indicates the parameters of the system as for instance pore radius, pore length etc.

The generic directory names is

<...> stands for a parameter. parameters:
	Geometry n (R_outer, R_mouth, L_mouth = 4A) 
		 1 = {15.5, 7.5}, 
		 2 = {18, 10}, 2a = {19.5, 10},  
		 3 = {26, 22}
		 4 = {25.8, 18}
	Length   l (L_pore):  8 A, 12 A
	Radius   r (R_pore):  3.5 ... 14 A	        		
	Charge   q
		 0    hydrophobic (no charge)
		 D1   one dipole (parallel z)
		 D2   two dipoles (both parallel z: down/down)
		 D2a  two dipoles (antiparallel z: up/down)
		 D4   four dipoles (all parallel z)
		 Q2   two quadrupoles
	Cavity   c: start with water filled (full) or empty (empty)
		 pore cavity

                 a unique name; I used it for runs starting with
                 different random seeds in the initial velocity

2 Files to be modified

You have to change:
mdp files: chl_emin.mdp, chl_md.mdp
The 'include' statement has to point to the directory which contains mth.itp and lay.itp unless they are already in Gromacs search path
NPROC: number of processors to generate tpr files for


Makefile contains a few other paths that are specific to my computer but you'll probably not need it anyway. You would need it (plus some other programs and scripts) if you wanted to generate input files and pdbs from scratch.
If you actually want to submit the jobs to a queuing system (we are using PBS here) you will have to edit a fair number of paths and the '#PBS -l' options for the number of nodes/processors used in rungmx.bash.

If everything is set up properly it is simply 'qsub rungmx.bash'.

3 Running a simulation

If everything is set up up properly you should be able to generate an input tpr file for the energy minimisation with
      make emin
Do the energy minimisation
      make run_emin
Generate an input tpr file for the MD
      make md
and start the simulation
      mpirun C -v -c2c -np 2 mdrun -np 2 -v \
                                   -s chl_md.tpr \
				   -deffnm chl_lay_water_md  
Please refer to the Makefile for the explicit syntax of the first three steps. You can also look through rungmx.bash: In the last quarter of the file (after lots of house keeping tasks) the same steps are executed.
Last modified: 2005-01-24 17:47:56+0000 by Oliver Beckstein