[gmx-users] Pull Code: direction-periodic with 3 dimensions
jalemkul at vt.edu
Fri Aug 11 23:05:34 CEST 2017
On 8/11/17 5:02 PM, Daniel Kozuch wrote:
> 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.
> 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
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users