Re: CNT modeling

From: Jonathan Lee (jonny5_at_rice.edu)
Date: Thu Jun 14 2007 - 14:44:32 CDT

FYI, I found about 10 angles that were defined incorrectly and I think
it's working correctly now. Thanks, everybody, for the help.

Jonathan

Jonathan Lee wrote:
> Hello,
>
> Since I generated my psf file myself (I wrote a Fortran code), I'm
> beginning to suspect that perhaps I missed some angles or dihedrals.
> Or perhaps I double-counted some. Is there a way to check this?
> If I have a chain of 4 atoms, 1-2-3-4, I count this as 2 angles,
> right? 1-2-3 and 2-3-4? Or if I have something like
>
> 4
> |
> 3-2-1
> |
> 4'
>
> this counts as 2 dihedrals? 1-2-3-4 and 1-2-3-4'? Thanks.
>
> Jonathan
>
>
> Alessio Alexiadis wrote:
>> Jonathan:
>> take a look to the "par_nanotubes.inp" file in the Namd tutorial
>> dedicated to CNTs and change it accordingly to your choices
>> Alessio
>>
>> */Jonathan Lee <jonny5_at_rice.edu>/* wrote:
>>
>> Hello Alessio,
>> Thank you, this is very helpful. But… how do I use this?
>> I’m using a CHARMM parameter file. Thanks.
>> Jonathan
>>
>> ------------------------------------------------------------------------
>> *From:* Alessio Alexiadis [mailto:sersunzo_at_yahoo.com]
>> *Sent:* Wednesday, June 13, 2007 12:07 AM
>> *To:* Jonathan Lee
>> *Subject:* Re: namd-l: CNT modeling
>> Dear Jonathan,
>> In my knowledge the issue is the angle bond rigidity, as you
>> mentioned; if it is too small the structure collapses.
>> The following values are often used to model CNTs
>> CHARMM AMBER
>> -------------------------------------------------------------------
>> r0 [°A] 1.375 1.4
>> kstretch[kcal mol−1°A−2] 305 469
>> -------------------------------------------------------------------
>> angle 120° 120°
>> kangle [kcal mol−1rad−2] 40 63
>> -------------------------------------------------------------------
>> n(dihedr) 2 2
>> fi0(dihedr) 180° 180°
>> kdihedr [kcal mol−1] 3.1 3.625
>> --------------------------------------------------------------------
>> sigmaC−C [°A] 3.55 3.4
>> epsilonC−C [kcal mol−1] 0.07 0.086
>> I hope this helps
>> Cheers
>> Alessio
>>
>>
>> */Jonathan Lee <jonny5_at_rice.edu>/* wrote:
>>
>> Hello all,
>> I am a new NAMD user. I am trying to simulate a solvated carbon
>> nanotube. I followed the basic procedure in the NAMD Tutorial of
>> Ubiquitin in a Water Sphere. However, after the simulation
>> completes, I
>> notice that the nanotube immediately collapses (forms an
>> oval-ish
>> cylinder shape). I repeated the exercise without any water
>> molecules
>> and the same thing happens. I'm wondering if there is an issue
>> with the
>> bond angle rigidity. Is there a way I can tweak that? Or does
>> anybody
>> have any other suggestions? Perhaps changing some parameters?
>> Thank you.
>>
>> Jonathan Lee
>>
>>
>>
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>
>
>

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