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

[Steven Neumann]

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
> >
> > ==================================================
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>