Hi, in gromacs 4 the pulling commands are part of the mdp file so copy the contents of your ppa file into your mdp file.
Alex V Hariharan schrieb: > 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 > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
