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

[aherz]

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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