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

[Justin Lemkul]

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.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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>>

-- 
==================================================

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

==================================================