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

[Erik Marklund]

Hi,

I believe there is no force output for constraint pulling. Try umbrella.

Erik

On Mar 18, 2013, at 3:28 PM, raghav singh wrote:

> 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
>
> ###############################################
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