[gmx-users] Gmx bundle regarding

Hi I have a 1000ns simulation of gpcr protein. The protein structure have 7 helix. 1. How will I calculate the tilt of each helix? 2. If it has to be done by generating the index file, what groups are meant to be added for index file? 3. What groups should be chosen when gmx bundle prompt to

Re: [gmx-users] gmx bundle

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 wrote: >

[gmx-users] gmx bundle

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