Re: [gmx-users] Time averaged ramachandran plot
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/-0003-3012-3557
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Re: [gmx-users] Time averaged ramachandran plot
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/-0003-3012-3557
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Time averaged ramachandran plot
Hey :)
That should use circ.awk:
{
x1 += sin($1)
x2 += cos($1)
}
END {
m = atan2(x1,x2)
print Number of points = NR
print Circular Mean = m
}
Otherwise, the mean of 180 and -180 gives you a 0 angle.
Cheers,
Tsjerk
On Mon, Oct 27, 2014 at 11:11 AM, andrea andrea.spital...@iit.it wrote:
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/-0003-3012-3557
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/GMX-Users_List before posting!
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https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
Tsjerk A. Wassenaar, Ph.D.
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[gmx-users] Time averaged ramachandran plot
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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
