README

Here are some tools to analyse a 3D pressure field calculated using a 
customised versions of Gromacs available from:
ftp://ftp.gromacs.org/pub/tmp/gromacs-4.0.2_localpressure.tar.gz 
http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
http://www.lacan.upc.edu/LocalStressFromMD


If you use the code, please cite:

Ollila et al. (2009) 
  3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes. 
  Phys. Rev. Lett. 102: 078101 [DOI: 10.1103/PhysRevLett.102.078101]

and

http://dx.doi.org/10.5281/zenodo.15666

SPHERICAL SYSTEM
---

compile:
  gcc -lm spherical_av.c -o spherical_av
use: 
  ./spherical_av local_pressure.dat

The code assumes that the center of your vesicle (origin of the spherical 
coordinate system) is in the center of the simulation box. So before 
running the pressure calculation you have to center it. If you have it not 
in the center but still not moving you can change the lines 149-151 in the 
code to redefine the COM.

Output in rad_pres.xvg is:
  distance from center (in voxel units)   P_theta   P_phi   P_r


PLANAR SYSTEM
---

compile:
  gcc -lm planar_av.c -o planar_av
use:
  ./planar_av local_pressure.dat

output:

  2Dlpp.dat
    Pressure tensor averaged over xy plane 
	(Pxx Pxy Pxz Pyx Pyy Pyz Pzx Pzy Pzz)

  3Dpp.dat
    Pressure tensor in 3D

  3Dppras.mol
    You can visualize 3D pressure opening this with rasmol and setting: 
	color->temperature and then use slab mode

  tension_radius.xvg
    Tension as a function from center of the system, averaged over angle in 
	cylindrical coordinates. Look Fig.3 in PRL paper.

  kappac0_radius.xvg
    Product of bending modulus and spontaneous curvature, averaged over 
	angle in cylindrical coordinates. Look Fig.3 in PRL paper.

  pres_prof_cil.xvg
    Using this with gnuscript you can plot similar figure than the Fig.3 a) 
	in the PRL paper.