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

[Alex]

What I meant is each of those files now has two columns, the first of 
which is of course time. What the second column is, especially for 
pullf, is a mystery to me. The total radial force? I wish someone who 
wrote the new pull code would clarify, because the result of wham now 
looks rather strange -- a long (1.5 nm!) hydration barrier for the ion. 
Makes little physical sense and very different from the bias along Z case.

I am guessing that the sampling of 1 ns per hemispherical slice is far 
from sufficient to probe that space... Just looked at one of the 
trajectories there -- the ion is nowhere near moving around the entire 
slice.

Alex


On 3/13/2018 10:27 AM, Justin Lemkul wrote:
>
>
> 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
>>>
>>
>