GROMACS version: 2020.3
GROMACS modification: No
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BS"D
Dear All,
We have a model of 4 polypeptides (each 12 residues long in our model) lying side by side (two parallel and two antiparallel) based on a crystal structure. These are known to undergo a conformational change when stretched, and we would like to model this in Gromacs. I have defined two pull groups, each being 4 terminal atoms in the chains, and I would like to pull the COM of each group in opposite directions, thus stretching the polypeptides. The coordinate file is set up so that the length of the chains is along Z. Here is what I prepared in the .mdp file. Since I don’t need to define the pull rate, I was wondering how to specify pulling in the -Z direction. I entered a “-1.0” value for the second pull vector. Is that correct? Should I be doing this differently?
Thanks
Harry
pull = yes
pull-print-com = yes
pull-print-ref-value = yes
pull-print-components = no
pull-pbc-ref-prev-step-com = no
pull-xout-average = no
pull-fout-average = no
pull-ngroups = 2
pull-ncoords = 2
pull-group1-name = END1
pull-group1-weights = 1 1 1 1
pull-group1-pbcatom = 0
pull-coord1-type = constant-force
pull-coord1-geometry = direction
pull-coord1-groups = 1 2
pull-coord1-dim = N N Y
;pull-coord1-origin =
pull-coord1-vec = 0.0 0.0 1.0
pull-coord1-k = 100
pull-group2-name = END2
pull-group2-weights = 1 1 1 1
pull-group2-pbcatom = 0
pull-coord2-type = constant-force
pull-coord2-geometry = direction
pull-coord2-groups = 1 2
pull-coord2-dim = N N Y
;pull-coord2-origin =
pull-coord2-vec = 0.0 0.0 -1.0
pull-coord2-k = 100