[gmx-users] g_sgangle not working as expected

[Yiannis]

There is a new option since last version. You have to add

-noone

otherwise the default -one is assumed (see last line of g_sgangle -h):

     -[no]one   bool    yes  only one group compute angle between vector 
at  time zero and t

To compute plane angles I use your second construction (two groups of 
three atoms each in the index file).

Yiannis


Le jeudi, 13 mai 2004, à 02:38 Europe/Paris, Scott Classen a écrit :

> 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?
>
> 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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