[gmx-developers] Merge enforced rotation branch into master

[Carsten Kutzner]

On Nov 17, 2010, at 11:35 AM, Berk Hess wrote:
> On 11/17/2010 11:33 AM, Carsten Kutzner wrote:
>> On Nov 16, 2010, at 10:42 PM, hess at sbc.su.se wrote:
>> 
>> 
>>> Hi,
>>> 
>>> A question on the mdp/inputrec options.
>>> I hope these are hidden when you don't use this, as for normal pull options.
>>> 
>> Hi Berk,
>> 
>> rotation options are analogous to pull options. The only extra
>> mdp option that is always there is of course
>> 
>> rotation = yes / no
>> 
>> I can also make the rotation output files in the mdrun file list hidden.
>> 
>> Carsten
>> 
> I thought rotation was a sub option of the pull options, but apparently
> it is not.
It is a separate section that allows to choose from 12 different rotation
potentials. Also the rotation vector, pivot, rate, spring constant, and
various other options depending on the type of potential are set. There
are e.g. variants mimicking a flexible axis by segmenting the rotation 
group into overlapping slabs and rotating each slab individually around
the local rotation axis centered in the slab's COM. Options like the slab
thickness can be set for that.

> How does it interact will the pull options then?
Not at all.

> Can you use pulling and rotation simultaneously?
Yes, you can have N pull groups and M rotation groups if
you like. Whether this makes sense is up to the individual
setup. If pull and rotation groups do not overlap, it is
never a problem. But you can also rotate a pull group 
while it is pulled (you have to choose the right rotation
potential, though). Makes sense to align the rotation and
pull vectors then. 

> I guess it should work fine when you pull and rotate the same groups,
> but they could interfere when the groups overlap partially.
The user has to think of course.

> PS I would like to change the pull groups such that there is not by
> definition
> a single reference group, but that can define general pairs.
I think that is a nice thing to have. This should
not interfere at all with the rotation code.

Carsten


> 
> Berk
>> 
>> 
>>> Berk
>>> 
>>> 
>>>> On Tue, Nov 16, 2010 at 17:58, Carsten Kutzner <ckutzne at gwdg.de> wrote:
>>>> 
>>>>> can I do a
>>>>> git checkout master; git merge release-4-5-patches; git push
>>>>> such that the master gets all the pending fixes from the
>>>>> 4.5 branch?
>>>>> 
>>>> It depends a bit on the context whether that works.  Assuming that you
>>>> have all the tracking branches created, what should work in all
>>>> situations is the following sequence:
>>>> git checkout release-4-5-patches
>>>> git pull
>>>> git checkout master
>>>> git pull
>>>> git merge release-4-5-patches
>>>> git push
>>>> Or alternatively, assuming that your remote repository has the default
>>>> name,
>>>> git checkout master
>>>> git pull
>>>> git merge origin/release-4-5-patches
>>>> git push
>>>> which gives identical history, but a bit different commit message on
>>>> the merge (that can also be edited manually).
>>>> 
>>>> Teemu
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>>>> 
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>> 
>> 
>> 
>> 
> 
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