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

[Berk Hess]

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: vhariharan2.gromacs at gmail.com
To: gmx-users at gromacs.org
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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