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

[Magnus Lundborg]

Hi Alex,

I don't think this is related to using pull-pbc-ref-prev-step-com. Have 
you tried without it? However, it is risky using pbcatom -1, since you 
don't know what atom you are using as the initial reference. I would 
suggest picking an atom you know is located at the centre of the structure.

I would think that the problem has to do with the comm removal. What are 
your parameters for comm-mode, nstcomm and comm-grps? It is possible 
that you need to lower your nstcomm. It is also possible, but not 
certain, the comm-mode Linear-acceleration-correction might help you. 
For some reason, it seems like I have sometimes avoided similar problems 
by using the sd integrator instead, but I haven't evaluated that 
properly - it might just have been coincidences. If you see a clear 
difference using the sd integrator it might be good if you'd file an 
issue about it on gitlab so that someone can look into if there is 
something wrong.

Regards,
Magnus

On 2020-04-18 20:12, Alex 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