Mark, thanks for responding. It seems like this is the second syntax
change for COM pulling since v. 4.6.x
If you don't mind my asking, why is this happening, esp. given no
backward compatibility? By comparing e.g. 5.0 and 5.1, I don't readily
see the rationale...
Peter, your suggested syntax works out of the box, thank you.
Alex
On 3/2/2016 2:16 AM, Mark Abraham wrote:
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 <[email protected]> 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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