[gmx-users] Artifact in pull-pbc-ref-prev-step-com

[Alex]

Dear all,
To generate the initial configurations for umbrella sampling, I conducted a
simple pulling simulation by which a single-small molecule (mol_A) is being
dragged along -Z from water into the body of a thin film.
Since the thin film is large I used *"pull-pbc-ref-prev-step-com = yes" and
"pull-group1-pbcatom      = -1"*  which cause a net shifting of the system
along the pulling direction as soon as the mol_A reach to the thin film,
please find below the pulling flags movie and  plot in below links.

Centering the thin film and mol_A could solve the issue,  (echo 1 0 |
trjconv -center yes) to some extent but still COM changes in the early
stage below 2ns. ,
COM:
https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0

Movie in which the water molecules are hidden:
https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv

-
gmx version 2020.1
-----
pull                     = yes
pull-print-com           = no
pull-print-ref-value     = yes
pull-print-components    = Yes
pull-nstxout             = 1000
pull-nstfout             = 1000
pull-pbc-ref-prev-step-com = yes
pull-ngroups             = 2
pull-ncoords             = 1
pull-group1-name         = Thin-film
pull-group1-pbcatom      = -1
pull-group2-name         = mol_A
pull-group2-pbcatom      = 0
pull-coord1-type         = umbrella
pull-coord1-geometry     = direction
pull-coord1-groups       = 1 2
pull-coord1-dim          = N N Y
pull-coord1-origin       = 0.0 0.0 0.0
pull-coord1-vec          = 0.0 0.0 -1.0
pull-coord1-start        = yes
pull-coord1-init         = 0
pull-coord1-rate         = 0.0005
pull-coord1-k            = 5000
-----
I wonder if I could extract correct initial configuration from this
trajectory? With correct initial configuration, I mean a set of gro file in
which change from one from to another is the distance between the COM of
the thin-film and mol_A?

Thank you
Alex