[gmx-users] Re: periodic molecule

[Valentina]

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.
> 
> 
>> 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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