[gmx-users] Pulling simulation

[Quyen Vu]

Hi Naveen,
I think you are looking for absolute reference position in space, which is
mention on page 436 of manual 2019.1
In my case, I pull ACE residue.
my pulling code is:
pull                    = yes
pull_ncoords            = 1         ; only one reaction coordinate
pull_ngroups            = 1         ; two groups defining one reaction
coordinate
pull_coord1_groups      = 0 1
pull_group1_name        = ACE
pull_coord1_type        = umbrella  ; harmonic potential
pull_coord1_geometry    = direction ; simple distance increase
pull-coord1-vec         = 1.0 0.0 0.0
pull_coord1_dim         = Y N N
pull_coord1_start       = yes       ; define initial COM distance > 0
pull-coord1-origin      = 18.0 5.19 5.06     ; absoulte reference point
pull_coord1_rate        = 0.005      ; 0.005 nm per ps = 5 nm per ns
pull_coord1_k           = 600      ; kJ mol^-1 nm^-2
;*********************************************************************************
Hope my code is useful with you or if I wrong, someone can correct me.
Best regards,
Quyen

On Mon, Apr 8, 2019 at 8:20 AM Naveen BK <naveenbk4717 at gmail.com> wrote:

> Dear all,
>
> This question is regarding Umbrella sampling. My group 1 is substrate and
> group 2 protein. Trying to pull the substrate molecule from the active site
> pocket. In all the cases(for group 2), I used either atom or residue for
> the center of mass [COM]. Now I want to run a simulation by considering
> that COM of protein which may be present in the vacuum or in the empty
> space. In other words, I don't want to fix any atom or residue of the
> protein but I want to fix an empty space. I was not able to find any
> solutions regarding this if anyone could help me to figure it, would be
> great.
>
> --
> Thanks and Regards,
> Naveen Krishna
> +91 8123474717
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