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
--
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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@.umaryland
| (410) 706-7441
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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