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

[Alex]

Hi Magnus,
Thanks.
The problem raises only because of using the pull-pbc-ref-prev-step-com
which needs the pull-group1-pbcatom to be -1 to be meaningful.
For an identical system and mdp parameters using 2018 version of gromacs
which is independent to the pull-pbc-ref-prev-step-com, I see no issue.

Regards,
Alex

On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg <
magnus.lundborg at scilifelab.se> wrote:

> Sorry, about the statement about pbcatom -1. I was thinking about 0. I
> don't know if pbcatom -1 is good or not in this case.
>
> Regards,
>
> Magnus
>
> On 2020-04-20 09:24, Magnus Lundborg wrote:
> > 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
> >
> >
>
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