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Tools to average pressures in 3D grid over different coordinate systems. Originally used in 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 shared http://md.chem.rug.nl/cgmartini/index.php/3d.
ohsOllila/pressure-tools
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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.
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Tools to average pressures in 3D grid over different coordinate systems. Originally used in 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 shared http://md.chem.rug.nl/cgmartini/index.php/3d.
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