GROMACS version: 2019
GROMACS modification: Yes/No
Hi
I was pulling a particle to a fixed point in the simulation box. but it didn’t work.
Here’s its error:
WARNING 1 [file md_pull.mdp]:
You are using an absolute reference for pulling, but the rest of the
system does not have an absolute reference. This will lead to artifacts.
How can I fix it?
Another question is about calculating the distance between fixed point and a particle (< groups.txt &>/dev/null is applicable for two groups).
pull = yespull-ncoords = 1
pull-group1-name = VO
pull-coord1-type = umbrella ;constant-force
pull-coord1-geometry = direction
pull-coord1-dim = N N Y
pull-coord1-vec = 0.0 0.0 1.0
pull-coord1-origin = 5 5 10
pull-coord1-start = yes
pull-coord1-rate = 0.01
pull-coord1-k = 1000
pull-coord1-groups = 0 1