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Hi,<br><br>Gromacs 4 no longer has ppa and pdo files.<br>The pull parameters are part of the mdp options, have a look at the manual.<br><br>Berk<br><br><hr id="stopSpelling">Date: Wed, 2 Sep 2009 09:40:56 -0400<br>From: vhariharan2.gromacs@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] Gromacs 4.0.4 - Pull.pdo File<br><br>Hello,<br><br>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.<br>
<br><br><br><b>.MDP FILE</b><br><br>title = MD Simulation<br>cpp = /lib/cpp<br>constraints = none<br>integrator = md<br>dt = 0.002<br>nsteps = 50000<br>nstcomm =<br>
nstxout = 200<br>nstxtcout = 200<br>nstvout = 0<br>nstfout = 1<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb =<br>
vdwtype = cut-off<br>rvdw =<br>fourierspacing =<br>fourier_nx =<br>fourier_ny =<br>fourier_nz =<br>pme_order =<br>ewald_rtol =<br>optimize_fft = yes<br>
pbc = xyz<br><br>; Berendsen Temperature Coupling<br>tcoupl = berendsen<br>tc-grps = protein non-protein<br>tau_t = 0.1 0.1<br>ref_t = 300 300<br><br>; Parinello-Rahman Pressure Coupling<br>
pcoupl = Parrinello-Rahman<br>pcoupltype = isotropic<br>tau_p = 1.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br><br>; Generate Velocities<br>gen_vel = yes<br>gen_temp = 300.0<br>
gen_seed = 173529<br><br><b>.PPA FILE</b><br><br>title = Pull Parameters for 3BPAdelDAL<br>pull = constraint<br>pull_geometry = distance<br>pull_dim = Y Y Y<br>pull_group0 = CTerminus<br>
pull_group1 = NTerminus<br><br><b>MDRUN COMMAND</b><br><br>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<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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