[gmx-users] Umbrella Pulling

[Justin A. Lemkul]

Steven Neumann wrote:
> Dear Justin and Gmx Users,
> 
> I run a pulling of my ligand away from my protein with the same mdp file 
> and I obtained two different plots - Force vs time (The breaking point 
> occured at different times with different force). Can you please explain?

If you change the stiffness of the spring, you change the magnitude of the 
applied force.  Thus, the behavior you see will occur either faster or slower, 
depending on the strength of the spring.

-Justin

> My mdp file:
> 
> title       = Umbrella pulling simulation
> define      = -DPOSRES_L
> ; Run parameters
> integrator  = md
> dt          = 0.002
> tinit       = 0
> nsteps      = 250000    ; 0.5ns
> nstcomm     = 10
> ; Output parameters
> nstxout     = 5000      ; every 10 ps
> nstvout     = 5000
> nstfout     = 500
> nstxtcout   = 500       ; every 1 ps
> nstenergy   = 500
> ; Bond parameters
> constraint_algorithm    = lincs
> constraints             = all-bonds
> continuation            = yes       ; continuing from NPT
> ; Single-range cutoff scheme
> nstlist     = 5
> ns_type     = grid
> rlist       = 0.9
> rcoulomb    = 0.9
> rvdw        = 0.9
> ; 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
> ; Temperature coupling is on
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc_grps     = Protein_LIG Water_and_ions   ; two coupling groups - more 
> accurate
> tau_t       = 0.1   0.1                     ; time constant, in ps
> ref_t       = 298   298                     ; reference temperature, one 
> for each group, in K
> ; Pressure coupling is on
> Pcoupl          = Parrinello-Rahman
> pcoupltype      = isotropic
> tau_p           = 1.0      
> compressibility = 4.5e-5
> ref_p           = 1.0
> ; Generate velocities is off
> gen_vel     = no
> ; Periodic boundary conditions are on in all directions
> pbc     = xyz
> ; Long-range dispersion correction
> DispCorr    = EnerPres
> ; Pull code
> pull            = umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim        = N N Y
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Protein
> pull_group1     = LIG182
> pull_rate1      = 0.016      ; 0.008 nm per ps = 8 nm per ns
> pull_k1         = 200      ; kJ mol^-1 nm^-2
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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