[gmx-users] GMX 2018 and 'distance' pull

[Justin Lemkul]

On 3/13/18 10:32 AM, Alex wrote:
> It appears that things have improved... I am just glancing and pullf 
> and pullx data from the first sample config and both contain only one 
> value, even though we set dim to 3D. Does this make sense?
>

I haven't used the 2018 pull code yet. Presumably this is correct, just 
the distance rather than all its components, though that would be a 
change from previous versions.

-Justin

> Thanks,
>
> Alex
>
> On 3/13/2018 8:18 AM, Justin Lemkul wrote:
>>
>>
>> On 3/13/18 10:17 AM, Alex wrote:
>>> Justin,
>>>>> You may have a situation that requires manual assignment of 
>>>>> pull_group1_pbcatom1, as the automatic choice of 
>>>>
>>>> Sorry, that should be pull_group1_pbcatom. Must remind myself not 
>>>> to email before coffee...
>>>>
>>> Did you mean pull_group2_pbcatom? In my case:
>>>
>>> pull_group1_name        = K
>>> pull_group2_name        = CNT
>>>
>>> The language for 5.1 pull is (you be the judge on how clear it is):
>>>
>>> pull-group1-pbcatom<http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html#mdp-pull-group1-pbcatom> 
>>>
>>>
>>>    (0) The reference atom for the treatment of periodic boundary
>>>    conditions inside the group (this has no effect on the treatment of
>>>    the pbc between groups). This option is only important when the
>>>    diameter of the pull group is larger than half the shortest box
>>>    vector. For determining the COM, all atoms in the group are put at
>>>    their periodic image which is closest topull-group1-pbcatom
>>> <http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html#mdp-pull-group1-pbcatom>. 
>>>
>>>    A value of 0 means that the middle atom (number wise) is used. This
>>>    parameter is not used withpull-group1-geometrycylinder. A value of
>>>    -1 turns on cosine weighting, which is useful for a group of
>>>    molecules in a periodic system,/e.g./a water slab (see Engin et al.
>>>    J. Chem. Phys. B 2010).
>>>
>>> Indeed, my group2 is a membrane that is wider than the shortest 
>>> half-box. I am assuming it would be a single atom belonging to the 
>>> pore region...
>>>
>>
>> Yes, pull_group2_pbcatom, not 1.
>>
>> -Justin
>>
>>> Thanks,
>>>
>>> Alex
>>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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