Hello,<br><br>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!<br><br>--Venk<br><br><div class="gmail_quote">On Wed, Sep 2, 2009 at 9:50 AM, aherz <span dir="ltr"><<a href="mailto:alexander.herz@mytum.de">alexander.herz@mytum.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br>
<br>
in gromacs 4 the pulling commands are part of the mdp file so copy the<br>
contents of your ppa file into your mdp file.<br>
<br>
Alex<br>
<br>
V Hariharan schrieb:<br>
<div><div></div><div class="h5">> Hello,<br>
><br>
> My .mdp file, .ppa file and mdrun command are provided below. After<br>
> running a constraint simulation, I am not getting a .pdo file output<br>
> with the forces between two groups I've specified in my .ppa file. I<br>
> have set a value for nstfout in the .mdp file (as shown), and used the<br>
> -pd option in the mdrun command. Anything I'm not seeing/doing<br>
> correctly? Since I've already run the simulation without getting a<br>
> .pdo output, is there any command to extract that data without<br>
> re-reunning the simulation? All suggestions are appreciated! Thanks.<br>
><br>
><br>
><br>
> *.MDP FILE*<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>
> *.PPA FILE*<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>
> *MDRUN COMMAND*<br>
><br>
> mdrun -s md.tpr -pi pull.ppa -pn index.ndx -x md_traj.xtc -po<br>
> kifpull.ppa -pd pull.pdo -o md.trr -c kif_md.pdb -e md.edr -g md.log<br>
</div></div>> ------------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote></div><br>