[gmx-users] umbrella versus constraint in the pulling code
Dr. Vitaly Chaban
vvchaban at gmail.com
Mon Dec 2 22:17:09 CET 2013
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.
Dr. Vitaly V. Chaban
On Mon, Dec 2, 2013 at 10:18 AM, Thomas Schlesier <schlesi at uni-mainz.de> wrote:
> 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.
> 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)
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