trj_analysis
The followings are the example of the distance calculation. Basically, same manners can be used in the case of angle and dihedral angle calculation.
Calculate the distance between Calpha atom in Residue 1 and Calpha atom in Residue 58
To calculate the distance between two atoms, we specify disfile in [OUTPUT], and select atom pairs by the parameters distance in [OPTION]. You can specify multiple distance pairs by distance1, distance2, …. In this care, the output file contains results in multiple columns.
[INPUT] psffile = ../BPTI_ionize.psf # protein structure file reffile = ../BPTI_ionize.pdb # PDB file [OUTPUT] disfile = output.dis # distance file [TRAJECTORY] trjfile1 = ../BPTI_run.dcd # trajectory file md_step1 = 500000 # number of MD steps mdout_period1 = 500 # MD output period ana_period1 = 500 # 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) [OPTION] check_only = NO # (YES/NO) distance1 = BPTI:1:ARG:CA BPTI:58:ALA:CA
If you do not like the above format in the atom selection, the following control file can be used, where the two atoms are selected by group1 and group2 in [SELECTION], and the center of mass distance is calculated by specifying com_distance in [OPTION] and comdisfile in [OUTPUT].
[INPUT] psffile = ../BPTI_ionize.psf # protein structure file reffile = ../BPTI_ionize.pdb # PDB file [OUTPUT] comdisfile = output.comdis # COM distance file [TRAJECTORY] trjfile1 = ../BPTI_run.dcd # trajectory file md_step1 = 500000 # number of MD steps mdout_period1 = 500 # MD output period ana_period1 = 500 # 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 = an:CA and rno:1 # select single atom group2 = an:CA and rno:58 # select single atom [OPTION] check_only = NO # (YES/NO) com_distance1 = 1 2
Calculate the center of mass distance between Residues 1 and 58
[INPUT] psffile = ../BPTI_ionize.psf # protein structure file reffile = ../BPTI_ionize.pdb # PDB file [OUTPUT] comdisfile = output.comdis # COM distance file [TRAJECTORY] trjfile1 = ../BPTI_run.dcd # trajectory file md_step1 = 500000 # number of MD steps mdout_period1 = 500 # MD output period ana_period1 = 500 # 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 = rno:1 # COM group 1 group2 = rno:58 # COM group 2 [OPTION] check_only = NO # (YES/NO) com_distance1 = 1 2