[gmx-users] Time averaged ramachandran plot

[andrea]

Hi,

on the fly try this using ALA1 as example (it can be any of your residues):

`grep -v '^#\|^@' rama.xvg | grep "ALA1" | awk '{if($2 == 0) print $2}' 
| awk -f std.awk


where std.awk contains:

{
   x1 += $1
   x2 += $1*$1
}
END {
   x1 = x1/NR
   x2 = x2/NR
   sigma = sqrt(x2 - x1*x1)
   if (NR > 1) std_err = sigma/sqrt(NR -1)
   print "Number of points = " NR
   print "Mean = " x1
   print "Standard Deviation = " sigma
   print "Standard Error = " std_err
}


hope it helps

and


On 27/10/2014 01:21, Justin Lemkul wrote:
>
>
> On 10/26/14 5:14 PM, Sanku M wrote:
>> Hi  I plan to plot the ramachandran plot of all the dihedral angles 
>> each of which is averaged over time-frames of trajectories. But, I 
>> find g_rama or g_chi gives the time profile of ramachandran plot. 
>> But, if I want to plot the time-averaged Phi.Psi angles of all 
>> residues, is there any method to do it.ThanksSanku
>>
>
> It's a process than can easily be written in any scripting language 
> you like. You have all the data points, and you want an average.  Just 
> post-process the output file with whatever kind of script (Perl, 
> Python, etc) you like.
>
> -Justin
>

-- 
-------------------------------------------------------
Andrea Spitaleri PhD
Principal Investigator AIRC
D3 - Drug Discovery & Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
http://www.iit.it/en/d3-people/andrea-spitaleri.html
ORCID: http://orcid.org/0000-0003-3012-3557