Hello, Thanks for the info. The information on page 280 of the GROMACS v4 manual making reference to the -pi -po -pd -pn options is what mislead me. Thanks again!
--Venk On Wed, Sep 2, 2009 at 9:50 AM, aherz <[email protected]> wrote: > 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 >
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