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

[Steven Neumann]

How about applying position restarints with a strong force constant? What
is less computationally expensive: position restrained, freezing the whole
molecule? The nanotube should be rigid... Shall I place the edged of the
tube on the box edge as well and use pbc=xyz and periodic molecules = yes?

Thanks,

Steven


On Thu, Sep 26, 2013 at 9:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<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 <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
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