[gmx-users] pull code in 5.1.2

[Alex]

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 <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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