[gmx-users] pull code in 5.1.2

[Mark Abraham]

Hi,

Yes, Google continues to find both the old and new documentation, while I
haven't found the time to migrate everything else to the new layout. The
documentation you found is marked as being for 5.0...

In general, seek documentation at http://manual.gromacs.org/documentation/.
I have updated the 5.1 release notes to be more specific on this particular
topic.

Mark



On Wed, Mar 2, 2016 at 9:57 AM Alex <nedomacho at gmail.com> wrote:

> Okay, I am officially the Jon Snow of COM pulling under 5.1.2. :) At the
> same time, neither the new manual, nor the google-preferred page
> (http://manual.gromacs.org/online/mdp_opt.html#pull) have the info you
> just linked to.
>
> Thanks a lot, let me try this.
>
> Alex
>
>
> On 3/2/2016 1:44 AM, Peter Kroon wrote:
> > Hi,
> > According to the manual
> > (
> http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html#com-pulling
> )
> > it should be something like this:
> >
> > pull = yes
> > pull-nstxout        = 1000
> > pull-nstfout        = 1000
> > pull_ngroups = 1
> > pull_group1_name = JON_SNOW_KNOWS_NOTHING
> > pull_ncoords = 1
> > pull-coord1-type = umbrella
> > pull_coord1_geometry = direction-periodic
> > pull_coord1_groups = 0 1 ; This means you are using an absolute
> > reference position (group 0).
> > pull_coord1_origin = 0 0 0 ; This is also the default value
> > pull_coord1_vec = 0 0 -1
> > pull_coord1_rate    = 5.0e-5
> > pull_coord1_k       = 1000
> > pull_coord1_start = yes
> >
> > Read the manual carefully, and make sure my suggestions are correct for
> > your case.
> > It might be nice to have a section in the manual (or a webpage) that
> > tells you how to translate between mdp versions.
> >
> > Peter
> >
> > On 02/03/16 07:48, Alex wrote:
> >> Hi all,
> >>
> >> In the Game of Thrones, as soon as you learn characters' names, they
> >> get brutally murdered. As soon as I got a good command of the pull
> >> code, an mdp working perfectly in 5.0.4 crapped its pants in 5.1.2
> >> (quoted below). The latest manual no longer even has a syntax section
> >> for pull code. 5.1.2 wasn't exactly my idea, we just got a new GPU
> >> node and the admin installed it. Roll back to older version?
> >>
> >> Thanks,
> >>
> >> Alex
> >>
> >> pull code section from a working mdp:
> >>
> >> ***
> >> pull                = umbrella
> >> pull_geometry       = direction-periodic
> >> pull_coord1_vec     = 0.0 0.0 -1.0
> >> pull_start          = yes
> >> pull_ngroups        = 1
> >> pull_ncoords        = 1
> >> pull_coord1_groups  = 0 1
> >> pull_group1_name    = JON_SNOWS_DEAD_BODY
> >> pull_coord1_rate    = 5.0e-5
> >> pull_coord1_k       = 1000
> >> pull-nstxout        = 1000
> >> pull-nstfout        = 1000
> >> ***
> >>
> >> Complaints below. Curiously, they all point to the same line, and that
> >> is a line nowhere near the pull code.
> >>
> >> WARNING 1 [file pull_300ns.mdp, line 51]:
> >>    Unknown left-hand 'pull_geometry' in parameter file
> >>
> >> WARNING 2 [file pull_300ns.mdp, line 51]:
> >>    Unknown left-hand 'pull_coord1_vec' in parameter file
> >>
> >> WARNING 3 [file pull_300ns.mdp, line 51]:
> >>    Unknown left-hand 'pull_start' in parameter file
> >>
> >> WARNING 4 [file pull_300ns.mdp, line 51]:
> >>    Unknown left-hand 'pull_ngroups' in parameter file
> >>
> >> WARNING 5 [file pull_300ns.mdp, line 51]:
> >>    Unknown left-hand 'pull_ncoords' in parameter file
> >>
> >> WARNING 6 [file pull_300ns.mdp, line 51]:
> >>    Unknown left-hand 'pull_coord1_groups' in parameter file
> >>
> >> WARNING 7 [file pull_300ns.mdp, line 51]:
> >>    Unknown left-hand 'pull_group1_name' in parameter file
> >>
> >> WARNING 8 [file pull_300ns.mdp, line 51]:
> >>    Unknown left-hand 'pull_coord1_rate' in parameter file
> >>
> >> WARNING 9 [file pull_300ns.mdp, line 51]:
> >>    Unknown left-hand 'pull_coord1_k' in parameter file
> >>
> >> WARNING 10 [file pull_300ns.mdp, line 51]:
> >>    Unknown left-hand 'pull-nstxout' in parameter file
> >>
> >> WARNING 11 [file pull_300ns.mdp, line 51]:
> >>    Unknown left-hand 'pull-nstfout' in parameter file
> >>
> >
> >
> >
>
> --
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