Hydrophobic Gating with Gromacs 3

OVERVIEW

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).

	Name	Last modified	Size	Description
	Parent Directory		-
	hygate.tar.bz2	2006-01-10 12:08	863K
	Readme.html	2012-01-02 19:52	5.3K
	Readme	2006-01-10 12:08	4.5K
	README.html	2012-01-02 19:52	4.5K
	HEADER.html	2012-01-02 19:52	1.7K

0 Unpack input files

  tar -jxvf hygate.tar.bz2
  cd HyGate

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 generic directory names is

  G<n>/L_<l>/<r>/<q>/<c>/<identifier>

	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

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

2 Files to be modified

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

Makefile.inc

NPROC: number of processors to generate tpr files for

Optional:

Makefile

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.

rungmx.bash

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

      make emin

      make run_emin

      make md

      mpirun C -v -c2c -np 2 mdrun -np 2 -v \
                                   -s chl_md.tpr \
				   -deffnm chl_lay_water_md  

SBCB   |  O.B.  |  Research  |  Publications  |  Software  |  Non-work