[gmx-users] Time averaged ramachandran plot

[andrea]

replace with this:

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



On 27/10/2014 11:04, andrea wrote:
> 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