[gmx-users] gmx bundle

[Mark Abraham]

Hi,

That means the calculation failed somehow (e.g. you asked for a dihedral
angle between four co-linear atoms, or divided by zero, or something like
that) but we don't have any clues on why (at this stage).

Mark

On Mon, Feb 1, 2016 at 6:22 AM Felix W.-H. Weng <weiweng013 at gmail.com>
wrote:

> Dear all:
>
> I'm trying to calculate kinks within alpha helices using gmx bundle. I
> specify 4 Ca atoms from the helix top, bottom and kink separately in the
> index file. And, I've used the option -na 1. But I keep getting the results
> shown below.
>
> @    title "Kink angles"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "(degrees)"
> @TYPE xy
>              0   -nan
>          500   -nan
>        1000   -nan
>        1500   -nan
>        2000   -nan
>        2500   -nan
>        3000   -nan
>        3500   -nan
>        4000   -nan
>        4500   -nan
>        5000   -nan
>             ...       ...
>
> Does anyone know what "-nan" implies? Any advice would be appreciated,
> thanks in advance.
>
>
>
> Best,
> Wei-Hsiang
> --
> Wei-Hsiang Weng (翁偉翔)
> Department of Life Sciences
> Tzu-Chi University
> No.701, Sec. 3, Zhongyang Rd. Hualien 97004, Taiwan
> Tel.: +886-975-232-245
> --
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