[gmx-users] Pull Code: direction-periodic with 3 dimensions
dkozuch at princeton.edu
Fri Aug 11 23:14:49 CEST 2017
Thanks for the quick reply, I was worried that was the case.
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
> > 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
> > 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.
> > 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
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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