GROMACS version: 2019.5
GROMACS modification: No
I have two peptide chains in a water box and I am running a pulling simulation with the following parameters:
pull = yes
pull_ncoords = 1
pull_ngroups = 2
pull-coord1-groups = 1 2
pull-group1-name = ChainA
pull-group2-name = ChainE
pull-coord1-type = umbrella
pull-coord1-geometry = direction-periodic
pull-coord1-vec = 1 1 1
pull-coord1-dim = Y Y Y
pull-nstxout = 1000
pull-nstfout = 1000
pull-pbc-ref-prev-step-com = yes
pull_coord1_start = yes
pull_coord1_rate = 0.0001
pull_coord1_k = 1000
pull-print-components = yes
I am getting the following pullx.xvg file (only shown first few lines):
@ s0 legend "1"
@ s1 legend "1 dX"
@ s2 legend "1 dY"
@ s3 legend "1 dZ"
0.0000 0.572965 0.0275484 1.00457 -0.0397192
2.0000 0.552969 -0.00228377 1.00714 -0.0470847
4.0000 0.568279 0.0204535 1.02422 -0.0603869
6.0000 0.575189 0.0152132 1.0322 -0.0511544
I think the last three columns correspond to the three components of the distance between the two pulling groups (I can confirm this using the tool gmx distance). However, I do not understand to what corresponds the second column.
Many thanks in advance.