[gmx-users] pull code - constraint pulling - forces are zeros

[raghav singh]

Hello Fellow Users,

I am trying to pull a DNA molecule. I have fixed one end and trying to pull
the other one using this .mdp file.. force output is all zeros.
I have tried going through the user-list but have not found any solution
yet. I am using gmx-version 4.5.5.

Any idea why is it happening.??
below is the mdp file i am using.

Thank you
Raghav

##############################################################

title       = constraint pulling simulation
define      = -DPOSRES
; Run parameters
integrator  = md
dt          = 0.002
tinit       = 0
nsteps      = 20000    ; 1ns
nstcomm     = 10
; Output parameters
nstxout     = 100      ; every 10 ps
nstvout     = 100
nstfout     = 20
nstxtcout   = 20      ; every 1 ps
nstenergy   = 20
energygrps  = DNA Water_and_ions
; Bond parameters
constraint_algorithm    = lincs
lincs_iter  = 1
lincs_order = 4
constraints             = all-bonds
continuation            = no       ; continuing from NPT
; Single-range cutoff scheme
nstlist     = 5
ns_type     = grid
rlist       = 1.2
rcoulomb    = 1.2
rvdw        = 1.2
; PME electrostatics parameters
coulombtype     = PME
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl      = V-rescale
tc_grps     = DNA       Water_and_ions
tau_t       = 0.1       0.1
ref_t       = 310       310
; Pressure coupling is on
Pcoupl          = Parrinello-Rahman
pcoupltype      = isotropic
tau_p           = 2.0
compressibility = 4.5e-5
ref_p           = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel     = yes
; Periodic boundary conditions are on in all directions
pbc     = xyz
; Long-range dispersion correction
DispCorr    = EnerPres
; Pull code
pull            = constraint
pull_geometry   = distance  ; simple distance increase
pull_dim        = N Y N
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Fixed
pull_group1     = Pull
pull_rate1      = 0.001      ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 500

###############################################