[gmx-users] Pull Code: direction-periodic with 3 dimensions

[Daniel Kozuch]

Thanks for the quick reply, I was worried that was the case.

Best,
Dan

On Fri, Aug 11, 2017 at 5:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/11/17 5:02 PM, Daniel Kozuch wrote:
> > Hello,
> >
> > I am using a pull code to increase the end-to-end distance of a protein
> > (included below). I am using direction-periodic and would like the
> distance
> > between the COM groups to be calculated in three dimensions. However,
> > setting pull_coord1_dim = Y Y Y appears to have no effect and the
> distance
> > printed to the pull file is still only in the pull_vec dimension (as
> > verified by checking with gmx distance). Is there any way to use
> > pull_coord1_dim = Y Y Y with direction-periodic?
> >
>
> No, because direction and direction-periodic only use pull_coord1_vec.
>
> http://manual.gromacs.org/documentation/2016.3/user-guide/
> mdp-options.html#com-pulling
>
> -Justin
>
> > pull                    = yes
> > pull_ngroups            = 2
> > pull_ncoords            = 1
> > pull_group1_name        = Chain_Begin
> > pull_group2_name        = Chain_End
> > pull_coord1_type        = umbrella      ; harmonic biasing force
> > pull_coord1_geometry    = direction-periodic
> > pull_coord1_groups      = 1 2
> > pull_coord1_dim         = Y Y Y
> > pull_coord1_rate        = 0.0
> > pull_coord1_k           = 5000          ; kJ mol^-1 nm^-2
> > pull_coord1_start       = no           ; define initial COM distance > 0
> > pull_coord1_init = 3.5
> > pull_coord1_vec         = 0 0 1
> >
> >
> > Thanks,
> > Dan
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
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> jalemkul at vt.edu | (540) 231-3129
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>
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