[gmx-users] Re: periodic molecule
jalemkul at vt.edu
Wed Sep 18 14:41:22 CEST 2013
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
>>> 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
>>> 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
>> 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)
>> How far apart are the atoms
>> across PBC, and how long is the assigned bond supposed to be? I have seen
>> cases posted to the list wherein the periodic_molecules function breaks
>> 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.
>>> threshold distances, that they rely upon? I really wouldn't like to have
>>> make the a bigger basic cell - too much topology assigning.
>> A bigger unit cell won't help. In fact, it would probably make things
>> Agree, thank you!
>> 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
>> gmx-users mailing list
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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.
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
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