[gmx-users] Nonsymetric molecule across pbc

[Steven Neumann]

Or maybe just 2 of them in the box: so that the one in the cell and another
one has its quarter in the unit cell edge and the free energy between them?
Then this PMF take into account all of the others being copied around.
Would US mdp option wont complain?

Steven


On Tue, Feb 18, 2014 at 7:49 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

>
> And the picture can be found here: http://speedy.sh/b73WM/Ssytem.png
>
>
> On Tue, Feb 18, 2014 at 7:49 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:
>
>> Thanks,
>>
>>  The picture is confidential so I will send it to you in the separate
>> msg. The distance between all tubes e.g. is 10 nm at the picture (I will
>> attach polypeptides to them later on). So I want to run window at this
>> distance... Then decrease it every 0.2 nm so all distances will decrease
>> between them...(3 tubes COM makes always isosceles traingle). I need to
>> pull all of them somehow closer to each other with some constraints or
>> distance restrarints I think...to reaach 9.8 nm etc.  So I wish that the
>> reaction coordinate would be the distance between all of their surfaces. Do
>> you know what I mean? Or maybe build something easier...they all matter and
>> will have influence on the distance... hence no clue which one of them
>> apply with harmonic potential...
>>
>> Steven
>>
>>
>> On Tue, Feb 18, 2014 at 7:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> On 2/18/14, 1:37 PM, Steven Neumann wrote:
>>>
>>>> Thanks a lot!
>>>> Can you please give me a hint how to apply umbrella sampling to the
>>>> system of 4
>>>> nanotubes with pbc across xyz so that they infinite in length in z
>>>> coordinate
>>>> and 2 of them placed with its half to the unit cell copied across y
>>>> coordinate...  I want to see PMF minima (equilibrium distance) between
>>>> their
>>>> centre of mass... With 2 nanotubes that would be easy (your tutorial)
>>>> but with 4
>>>> of them? I am thinking of changing the distance between and run windows
>>>> but no
>>>> clue which group setup as group0 and group1...
>>>>
>>>>
>>> It's not clear what your objective really is, and I'm sorry to say that
>>> I find your description to be very confusing.  A picture would help.  What
>>> is your reaction coordinate?  Are you trying to determine the free energy
>>> profile for one tube in relation to another, with 2 others as bystanders,
>>> or do the other 2 serve some functional role?  If you're looking to do a
>>> multidimensional WHAM, you'll have to approach each reaction coordinate
>>> individually.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
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>>
>