[gmx-users] Gromacs 4.0.4 - Pull.pdo File

[V Hariharan]

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 <alexander.herz at mytum.de> 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
> > ------------------------------------------------------------------------
> >
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