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

Dr. Vitaly Chaban vvchaban at gmail.com
Thu Sep 26 16:19:41 CEST 2013

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.


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
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