[gmx-users] carbon nanotube - ifnite in length ?

[Dr. Vitaly Chaban]

Steven -

I would use a simple harmonic bond.


Dr. Vitaly V. Chaban


On Thu, Sep 26, 2013 at 5:12 PM, Steven Neumann <s.neumann08 at 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 <vvchaban at 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 <jalemkul at 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
>> >
>> > --
>> > ==================================================
>> >
>> > 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
>> >
>> > ==================================================
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