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

[V Hariharan]

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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