[gmx-users] Re: periodic molecule

[Justin Lemkul]

On 9/18/13 8:34 AM, Valentina wrote:
> Justin Lemkul wrote
>> On 9/18/13 8:07 AM, Valentina wrote:
>>> Thank you!
>>>
>>> Yep, they seem to be wanting to bond to the O's within the cell, while
>>> they
>>> are meant to bond across the PBC.
>>>
>>> I am not sure how periodic_molecule = yes part functions. I don't seem to
>>> get difference if I turn it on or off when I do Energy minimisation. Do
>>> you
>>> have some examples that work, so I can compare to them? Are there some
>>
>> I have never used periodic molecules, except when toying around with some
>> CNTs
>> for my own curiosity.  I suspect the problem you're seeing arises from the
>> bonded atoms being closer within the unit cell than they are across PBC,
>> so the
>> minimum distance is what is trying to be satisfied.
>>
>>
>>
>> Nope, thats not the case.
>> Across pbc it's 2.06A while across the cell it's 7.89A (see the attached
>> pic, where in bold are the atoms whitin the cell and small are the
>> periodic representation it should bond to)
> <http://gromacs.5086.x6.nabble.com/file/n5011279/Screen_Shot_2013-09-18_at_13.30.23.png>
>>
>> How far apart are the atoms
>> across PBC, and how long is the assigned bond supposed to be?  I have seen
>> other
>> cases posted to the list wherein the periodic_molecules function breaks
>> down
>> simply because of bad starting geometry.
>>

Can you please address this question regarding the desired bond length, as well? 
  If the distance is not within the normal tolerance (10%), then a bond will not 
be detected across PBC and thus will default to forming within the unit cell.

-Justin

>>
>>> threshold distances, that they rely upon? I really wouldn't like to have
>>> to
>>> make the a bigger basic cell - too much topology assigning.
>>>
>>
>> A bigger unit cell won't help.  In fact, it would probably make things
>> worse.
>>
>> Agree, thank you!
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> 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 .umaryland
>
>>   | (410) 706-7441
>>
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> View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011279.html
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>

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

Justin A. Lemkul, Ph.D.
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

==================================================