Hi,
Gromacs 4 no longer has ppa and pdo files.
The pull parameters are part of the mdp options, have a look at the manual.
Berk
Date: Wed, 2 Sep 2009 09:40:56 -0400
From: [email protected]
To: [email protected]
Subject: [gmx-users] Gromacs 4.0.4 - Pull.pdo File
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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