Hi all!
I have a question about how g_angle works. Form what I understood from
the manual, if I provide an index file with dihedral quadruplets, then
g_angle with the options -ov -all and -type dihedral should give me a
list of dihedral values one for each quadruplet. However when I do
that I obtai
Thank you. It worked now.
Best
Francesca
2012/2/29 Mark Abraham :
> On 1/03/2012 1:00 AM, francesca vitalini wrote:
>>
>> Hi Mark,
>> Thanks for your answer. What I'm trying to do is calculate the value
>> in degrees of the angles listed in my index file. If my index file
>> looks like
>> [ dih
On 1/03/2012 1:00 AM, francesca vitalini wrote:
Hi Mark,
Thanks for your answer. What I'm trying to do is calculate the value
in degrees of the angles listed in my index file. If my index file
looks like
[ dihedral 1 ]
2 7 9 10
[ dihedral 2 ]
10 16 18 19
I said in my last email that my s
Hi Mark,
Thanks for your answer. What I'm trying to do is calculate the value
in degrees of the angles listed in my index file. If my index file
looks like
[ dihedral 1 ]
2 7 9 10
[ dihedral 2 ]
10 16 18 19
then if I use the command line
g_angle -f aa.gro -s aa.tpr -n angles_prova.ndx -ov a
On 29/02/2012 11:54 PM, francesca vitalini wrote:
2012/2/29 Mark Abraham:
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 1
hi francesca,
i think what you are looking for is this
g_sgangle $indexFile -f $traj -s $tpr -oa $outfile
before that, you have to define two planes (by 3 atom indices each) in
your index file
[ dihed1 ]
523 680 3482
[ dihed2 ]
680 3482 3691
which you choose when having started g_sgangle.
2012/2/29 Mark Abraham :
> 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 mig
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.
However it produces a .xvg file whe
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
.
However it produces a .xvg file where it gives me for each angle in
degrees its probability. However, what I want is in
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