[gmx-users] gmx bundle

Felix W.-H. Weng weiweng013 at gmail.com
Mon Feb 1 06:21:54 CET 2016

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.

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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