[gmx-users] pull code in 5.1.2

[Peter Kroon]

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
>