Hello, My .mdp file, .ppa file and mdrun command are provided below. After running a constraint simulation, I am not getting a .pdo file output with the forces between two groups I've specified in my .ppa file. I have set a value for nstfout in the .mdp file (as shown), and used the -pd option in the mdrun command. Anything I'm not seeing/doing correctly? Since I've already run the simulation without getting a .pdo output, is there any command to extract that data without re-reunning the simulation? All suggestions are appreciated! Thanks.
*.MDP FILE* title = MD Simulation cpp = /lib/cpp constraints = none integrator = md dt = 0.002 nsteps = 50000 nstcomm = nstxout = 200 nstxtcout = 200 nstvout = 0 nstfout = 1 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = vdwtype = cut-off rvdw = fourierspacing = fourier_nx = fourier_ny = fourier_nz = pme_order = ewald_rtol = optimize_fft = yes pbc = xyz ; Berendsen Temperature Coupling tcoupl = berendsen tc-grps = protein non-protein tau_t = 0.1 0.1 ref_t = 300 300 ; Parinello-Rahman Pressure Coupling pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate Velocities gen_vel = yes gen_temp = 300.0 gen_seed = 173529 *.PPA FILE* title = Pull Parameters for 3BPAdelDAL pull = constraint pull_geometry = distance pull_dim = Y Y Y pull_group0 = CTerminus pull_group1 = NTerminus *MDRUN COMMAND* mdrun -s md.tpr -pi pull.ppa -pn index.ndx -x md_traj.xtc -po kifpull.ppa -pd pull.pdo -o md.trr -c kif_md.pdb -e md.edr -g md.log
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