[gmx-users] fail to pull

[Justin Lemkul]

On Sat, Apr 6, 2013 at 2:47 PM, Albert <mailmd2011 at gmail.com> wrote:

> Dear:
>
>  I am trying to pull my ligand outside of the binding pocket with
> following configurations:
>
> title       = Umbrella pulling simulation
> define      = -DPOSRES
> ; Pull code
> pull            = umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim        = Y N N
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Protein
> pull_group1     = LIG
> pull_rate1      = 0.001      ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 1000      ; kJ mol^-1 nm^-2
>
> Tcoupl      = v-rescale
> tc_grps     = Protein_LIG   Water_and_ions
> tau_t       = 0.5       0.5
> ref_t       = 310       310
> ; Pressure coupling is on
> Pcoupl          = Parrinello-Rahman
> pcoupltype      = isotropic
> tau_p           = 1.0   1.0
> compressibility = 4.5e-5
> ref_p           = 1.0     1.0
> refcoord_scaling = com
> ; Generate velocities is off
> gen_vel     = no
> ; Periodic boundary conditions are on in all directions
> pbc     = xyz
> ; Long-range dispersion correction
> DispCorr    = EnerPres
>
>
>
> It is quite strange, the ligand is still in place and not outside the
> pocket at the end of simulations. I am just wondering where is the problem?
>
>
Hard to tell. Does your ligand have a suitable exit pathway exactly aligned
along the x-axis? Have you tried increasing the pull rate? How long is the
simulation? I don't even see nsteps in the above .mdp file. How about
increasing the force constant? Is the vector connecting the COM of the
entire protein and the COM of the ligand suitable for describing the exit
pathway?

-Justin

-- 

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

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