[gmx-users] g_sgangle not working as expected

[David van der Spoel]

On Thu, 2004-05-13 at 02:38, Scott Classen wrote:
> Hello GROMACers,
> I am trying to monitor a specific dihedral angle as a function of time 
> in my MD simulation.
> I have the following atoms for example.
> 
> A-B-C-D
> 
> I have tried doing this by defining 2 vectors in my custom index.ndx 
> file
> [vec1]
> B A
> [vec2]
> C D
> 
> I have also tried defining two planes such as this:
> [vec1]
> C B A
> [vec2]
> B C D
> 
> Either way when I run g_sgangle I am only asked to select one group and 
> the program appears to do some sort of self??? analysis.
> Am I doing something wrong?

you need to give an additional option: -oa

> 
> Here is a snippet of the output:
> 
> Reading file icrf187-water-md.tpr, VERSION 3.2.1 (single precision)
> Group     0 (        vec1) has     3 elements
> Group     1 (        vec2) has     3 elements
> Select a group: 0 1
> Selected 0: 'vec1'
> 
> Group vec1 contains the following atoms:
> Atomname 0: CAI
> Atomname 1: N
> Atomname 2: CAO
> 
> Group vec1 contains the following atoms:
> Atomname 0: CAI
> Atomname 1: N
> Atomname 2: CAO
> 
> Careful: distance only makes sense in some situations.
> 
> Reading frame       0 time    0.000
> 
> Last frame        100 time  100.000
> 
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>    Scott Classen, Ph.D.
>    ACS Postdoctoral Fellow
>    Department of Molecular & Cell Biology
>    University of California, Berkeley
>    237 Hildebrand Hall #3206
>    Berkeley, CA 94720-3206
>    LAB 510.643.9491
>    FAX 510.643.9290
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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