[gmx-users] pull code in 5.1.2

[Alex]

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
>>
>
>
>