From: Jonathan Lee (jonny5_at_rice.edu)
Date: Wed Jun 13 2007 - 13:02:58 CDT
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? Â
> 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
>
> Â
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