[gmx-users] umbrella versus constraint in the pulling code

[Dr. Vitaly Chaban]

Hi Thomas -

I would also expect that it works the same way as before and as
described in the manual. However, thus far I am not very successful.
The main application of the "constraint" option is probably to
automatically get evenly spaced windows during pulling, but I am not
able to achieve this. It is quite mysterious.

Vitaly

Dr. Vitaly V. Chaban


On Mon, Dec 2, 2013 at 10:18 AM, Thomas Schlesier <schlesi at uni-mainz.de> wrote:
> Hi,
> I never used the pull-code with GMX 4.5.x or 4.6.x,but I would assume that
> it'sthe same as in 4.0.x:
> 'Umbrella': Due to the harmonic potential the force and the distance between
> the two particles will fluctuate.
> 'Constraint': Only the force will fluctuate. The (relative) distance between
> the two particles should either stay constant (if v=0) or increase linearly
> (v.ne.0). But still the position of both groups can fluctuate, but only in
> such a way that the constraint isn't violated.
> Greetings
> Thomas
>
>
> Am 30.11.2013 15:41, schrieb
> gromacs.org_gmx-users-request at maillist.sys.kth.se:
>>
>> Could anyone please explain the difference between how "umbrella" and
>> "constaint" options in the pulling code work. Based on the manual, I
>> expect that the only difference
>> is that umbrella used harmonic potential to bind pulled group to the
>> reference group (point), while "constraint" uses shake algorithm to
>> rigidly bind the groups. However, the simulations shows that this is
>> not true. With all other options being the same, umbrella provides
>> expected pulling, while constraint exhibits rather fluctuations of the
>> pulled group nearby starting position. What do I miss?
>>
>> Dr. Vitaly V. Chaban
>>
>> output from the "constraint" simulation with moving reference point
>> (i.e. pull_geometry = position)
>> z-coordinate
>>   6.38675
>>   5.97254
>>   5.88948
>>   5.86992
>>   5.72523
>>   5.59002
>>   5.84313
>>   5.83232
>>   5.88722
>>   5.83665
>>   6.00198
>>   5.96873
>>   5.57108
>>   5.35213
>>   5.47916
>>   5.46968
>>   5.40241
>>   5.41725
>>   5.4732
>>   5.45464
>>   5.61582
>>   5.66366
>>   5.8005
>>   5.9086
>>   6.10943
>>   6.11296
>>   6.21684
>>   5.95532
>>   5.89226
>>   6.00983
>
>
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