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

[Justin Lemkul]

On 3/13/18 4:19 PM, Alex wrote:
> 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 

It's the force on the spring connecting the two groups.

-Justin

> 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
>>>>
>>>
>>
>

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

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

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340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
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