CV Usage -------- The following are a few examples of using CVs for an ABMD simulation: To use CVs in simulation, we need to add the namelist &abmd(for ABMD) or &smd(for SMD) in the mdin file, and also put the CV variables in another file to be read. For example, if we want to use DISTANCE between two atoms as the CV for SMD and ABMD simulation, we can create a new file cv.in with &colvar npath = 2, nharm = 1, path = 8.0, 5.0, harm = 10.0 cv_type = 'DISTANCE' cv_min = 3.0, cv_max = 10.0, resolution = 1.0 cv_ni = 2, cv_i = 5, 8, / To run SMD, we can add the following &smd section to mdin file &smd output_file = 'smd.dat' output_freq = 1 cv_file = 'cv.in' / To run ABMD, we can add the following &abmd section to mdin file &abmd mode = 'FLOODING' monitor_file = 'monitor.txt' monitor_freq = 1 umbrella_file = 'umbrella.nc' timescale = 1.0 wt_temperature = 10000.0 wt_umbrella_file = 'wt_umbrella.nc' cv_file = 'cv.in' / Also you can run a more complicated case with two CVs. In this case, you just need to add another &colvar section in the cv input file. For example, if you have another CV COS_OF_DIHEDRAL, you can write the cv.in file like: &colvar npath = 2, nharm = 1, path = 8.0, 5.0, harm = 10.0 cv_type = 'DISTANCE' cv_min = 3.0, cv_max = 10.0, resolution = 1.0 cv_ni = 2, cv_i = 5, 8, / &colvar cv_type = 'COS_OF_DIHEDRAL' ! sum of cosines of dihedral angles cv_ni = 8 cv_i = 2, 5, 7, 17, 17, 19, 21, 31, path = -5.0, -4.0, -4.0, -5.0 npath = 4 harm = 100.0 nharm = 1 cv_min = -2, cv_max = 2, resolution = 0.5, /