On 29/02/2012 11:54 PM, francesca vitalini wrote:
2012/2/29 Mark Abraham<mark.abra...@anu.edu.au>:
On 29/02/2012 9:39 PM, francesca vitalini wrote:
Hi all,
I'm trying to use g_angle to calculate a list of dihedrals that I have
into an hand made index file (angles.ndx), which looks like
[ dihedrals ]
2 5 9 10
10 15 18 19
.....
mk_angndx might have helped.
Actually mk_angndx gies me the angles for phi and psi while instead I
need omega and they are put in a strange format like in groups of 8
instead of 4.
Whitespace inside the index group probably doesn't matter.
However it produces a .xvg file where it gives me for each angle in
degrees its probability. However, what I want is instead to know the
value in degrees of each angle in the ndx file. Do you have any
suggestions apart from building an index file for each angle?
g_angle -ov -all with each angle in its own group.
What do you mean with each angle in its own group? something like
[dihedrals]
2 5 9 10
[dihedrals]
10 13 16 18
...
Yes, but with unique group names - but it turns out I was wrong to
suggest that. Your index file above is fine.
Isn't it equivalent to build differend index files?
anyway the -ov flag gives the average over time, but I need the angles
just at one time, that is why I was using -od but it just plots the
distribution of all angles together.
Any help?
Which part of the output of g_angle -ov **-all** doesn't suit you?
Mark
Thanks
Mark
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