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

[Alex]

Any comment on this would be so appreciated!

Regards,
Alex

On Sat, Apr 18, 2020 at 2:12 PM Alex <alexanderwien2k at gmail.com> wrote:

> 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
>