[gmx-users] what is theta in g_helixorient?

Albert mailmd2011 at gmail.com
Tue Oct 2 17:35:42 CEST 2012

On 10/02/2012 05:16 PM, Justin Lemkul wrote:
> On 10/2/12 11:13 AM, Albert wrote:
>> hello guys:
>>    I am using g_helixorient to analyze the helix property in my 
>> system and it
>> generate three theta[1,2,3].xvg  file. I am wondering what's that? I 
>> didn't find
>> any comments in the help file.
> Have you read the last paragraph of g_helixorient -h?
> -Justin

of course, here it is. I don't find anything related to my questions.

Option     Filename  Type         Description
   -s      topol.tpr  Input        Run input file: tpr tpb tpa
   -f       traj.xtc  Input        Trajectory: xtc trr trj gro g96 pdb cpt
   -n      index.ndx  Input, Opt.  Index file
-oaxis  helixaxis.dat  Output       Generic data file
-ocenter center.dat  Output       Generic data file
-orise     rise.xvg  Output       xvgr/xmgr file
-oradius radius.xvg  Output       xvgr/xmgr file
-otwist   twist.xvg  Output       xvgr/xmgr file
-obending    bending.xvg  Output       xvgr/xmgr file
-otilt     tilt.xvg  Output       xvgr/xmgr file
-orot  rotation.xvg  Output       xvgr/xmgr file

Option       Type   Value   Description
-[no]h       bool   yes     Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    19      Set the nicelevel
-b           time   0       First frame (ps) to read from trajectory
-e           time   0       Last frame (ps) to read from trajectory
-dt          time   0       Only use frame when t MOD dt = first time (ps)
-xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-[no]sidechain bool no      Calculate sidechain directions relative to helix
                             axis too.
-[no]incremental bool   no      Calculate incremental rather than total

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