This tool analyzes the coordinates of the center of mass of the selected atoms or molecules.
# Center of mass of the selected group analysis_for = ALL # Center of mass of each molecule in the selected group analysis_for = MOLECULE
XY-coordinates of the center of mass of lipid molecules around membrane proteins
The output file contains the trajectory of the xy-coordinates of each lipid molecules. The users can visualize lateral movement of the lipid molecules, and analyze the lateral diffusion of the molecules around the membrane protein.
[INPUT] psffile = ../RALP_DPPC.psf reffile = ../RALP_DPPC_run.pdb [OUTPUT] trjfile = output.trj # trajectory file [TRAJECTORY] trjfile1 = ../RALP_DPPC_run.dcd # trajectory file md_step1 = 1000 # number of MD steps mdout_period1 = 1 # MD output period ana_period1 = 1 # analysis period repeat1 = 1 trj_format = DCD # (PDB/DCD) trj_type = COOR+BOX # (COOR/COOR+BOX) trj_natom = 0 # (0:uses reference PDB atom count) [SELECTION] group1 = segid:PROA # membrane protein group2 = rnam:DPPC # lipid [FITTING] fitting_method = TR # fitting the membrane protein by translation fitting_atom = 1 # membrane protein mass_weight = NO # mass-weight is not applied [OPTION] check_only = NO centering = NO analysis_atom = 2 # select lipid analysis_for = MOLECULE # center of mass of molecules is analyzed output_coord = XY # XY-coordinates of the center of mass pbc_correct = NO # no wrap molecule