On 9/26/13 12:05 PM, Dr. Vitaly Chaban wrote:
Steven -
I would use a simple harmonic bond.
Note that either in the case of the distance restraint or harmonic interaction
approach, both the CNT and the molecule to which it is tethered need to be in
the same [moleculetype], so run pdb2gmx (or whatever you are using) with care.
-Justin
Dr. Vitaly V. Chaban
On Thu, Sep 26, 2013 at 5:12 PM, Steven Neumann <s.neuman...@gmail.com> wrote:
Thank you for this. And also I wish to attach a chain to my nanotube so they
will be both able to move together. Is that a matter of distance restraints
between nanotube atom and first atom of my chain or again - LINCS? Both
chain and nanotube are made of the same type of 8 type of atoms. Please,
advise.
Steven
On Thu, Sep 26, 2013 at 3:19 PM, Dr. Vitaly Chaban <vvcha...@gmail.com>
wrote:
I am just curious why the system would explode without
"periodic_molecules = yes". If the PBC procedure is applied before
harmonic bond potential is calculated, than the opposite nanotube
atoms should be (already) seen as neighboring. This looks the same as
the solvent molecule, one atom of which crossed the box boundary.
No?
Dr. Vitaly V. Chaban
On Thu, Sep 26, 2013 at 3:59 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 9/26/13 8:39 AM, Steven Neumann wrote:
Dear Gmx Users,
I have my carbon nanotube and I wish to make it infinite in lenght.
Which
mdp options whall be used? pbc = xy and z is the infinite dimension?
another issue: Would you apply bonds between carbon atoms within the
nanotube or constraints using LINCS? Which of them is less
computationally
expensive for the run?
Use "pbc = xyz" in conjunction with "periodic_molecules = yes" otherwise
the
topology gets messed up trying to form unreasonable bonds. The
periodic_molecules keyword in the .mdp allows for bonds to be maintained
over PBC.
I remember a very old post somewhere in the archive that said one should
not
apply pressure coupling along the axis of the nanotube, due to some
difficulties with maintaining the bonded geometry, but since I have
never
done CNT simulations, take the fact that I'm just repeating what I've
heard
for what it's worth :)
Constraints always come with the cost of communication, so I would
imagine
harmonic bonds are "less expensive." I really don't see constraints as
a
limiting factor for performance, though.
-Justin
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Justin A. Lemkul, Ph.D.
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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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