[gmx-users] Umbrella Pulling

[Steven Neumann]

On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
>
So how can I change the stiffness of my spring?

Steven

>
>  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
>>
>>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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