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

[Steven Neumann]

And also ... my tube has 1200 atoms and I wish to apply [ exclusions ] - is
there any gmx tool to exclude interactions within the given molecule so 1
with all 1200, 2 with all 1200...etc... 1200 with all 1200?

Steven


On Thu, Oct 10, 2013 at 2:34 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> Thanks a lot. You the bond as a distance between atoms? I wish to avoid
> bonds as they are not necessary...just position restraint. What would be
> the force constant? I tried 1000 once without bonds and my atoms were
> moving a bit...
>
> Steven
>
>
> On Thu, Oct 10, 2013 at 2:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/10/13 9:21 AM, Steven Neumann wrote:
>>
>>> 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
>>>
>>
>> You shouldn't see any real performance gain or loss by applying either
>> restraints or freezing.
>>
>>
>>  tube on the box edge as well and use pbc=xyz and periodic molecules =
>>> yes?
>>>
>>>
>> The box size needs to be (length of tube) + (bond length).  If you place
>> the carbon atoms at the box edge, they overlap and the system blows up.
>>
>>
>> -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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