Dear all
When I use the following command:
g_analyze -ffree_bi_0.9.xvg -av average_0.9
I got
set average standard deviation *std. dev. /
sqrt(n-1)*…
SS16.053822e+01 3.062230e+01 1.936724e-02…
What is “*std. dev. / sqrt(n-1)”
On 4/16/13 4:47 PM, Ahmet yıldırım wrote:
First column is time, second is rmsd value and third column is 0.
average.xvg
10 0.3123 0
20 0.3256 0
30 0.3981 0
40 0.3512 0
50 0.3754 0
...
I see. It seems that g_analyze deals well with some files and not others. If,
for instance, I analyze a h
First column is time, second is rmsd value and third column is 0.
average.xvg
10 0.3123 0
20 0.3256 0
30 0.3981 0
40 0.3512 0
50 0.3754 0
...
2013/4/16 Justin Lemkul
>
>
>
> On 4/16/13 4:26 PM, Ahmet yıldırım wrote:
>>
>> Dear users,
>>
>> g_analyze -f rmsd.xvg -av average.xvg -errbar stddev
>>
On 4/16/13 4:26 PM, Ahmet yıldırım wrote:
Dear users,
g_analyze -f rmsd.xvg -av average.xvg -errbar stddev
Unfortunately, this command didn't produce the error bar
How can I obtain error bar for plotting?
Works fine for me. Perhaps you're just not plotting average.xvg correctly.
Import as
Dear users,
g_analyze -f rmsd.xvg -av average.xvg -errbar stddev
Unfortunately, this command didn't produce the error bar
How can I obtain error bar for plotting?
Thanks in advance
--
Ahmet Yıldırım
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-
Dear users, I have a question concerning g_analyze:
I have N similar time-dependent datasets, calculate autocorrelation
functions using "g_analyze -f -ac -n -nosubav" and get N results. I
found that the program can also be called with the option -oneacf, but
was not able yet to find out, what thi
Dear Gromacs Specialists,
I have one problem about g_analyze -ee, May I ask you to help me, Please?
When I do this program as "g_analyze -f .xvg -av -ee", it is as followed:
Read 4 sets of 83001 points, dt = 6
std. dev. relative deviation of
Dear Justin,
Thank you very much from your response.
Best Regards
Dina
From: Justin A. Lemkul
To: dina dusti ; Discussion list for GROMACS users
Sent: Monday, February 20, 2012 11:07 PM
Subject: Re: [gmx-users] g_analyze -ee
dina dusti wrote:
> D
y for thank
from you.
Best Regards
Dina
*From:* Justin A. Lemkul
*To:* dina dusti ; Discussion list for GROMACS
users
*Sent:* Saturday, February 18, 2012 5:29 PM
*Subject:* Re: [gmx-users] g_analyze -ee
dina dusti
thank from you.
Best Regards
Dina
From: Justin A. Lemkul
To: dina dusti ; Discussion list for GROMACS users
Sent: Saturday, February 18, 2012 5:29 PM
Subject: Re: [gmx-users] g_analyze -ee
dina dusti wrote:
> Dear Gromacs Specialists,
>
> Sometime
dina dusti wrote:
Dear Gromacs Specialists,
Sometimes, when I do "g_analyze -f .xvg -av -ee error.xvg" , I take
following warning, and I don't know how to fix it.
Set 1: err.est. 0.000596502 a 0.29217 tau1 24.8856 tau2 443.641
Warning: tau2 is longer than the length of the data (
Dear Gromacs Specialists,
Sometimes, when I do "g_analyze -f .xvg -av -ee error.xvg" , I take
following warning, and I don't know how to fix it.
Set 1: err.est. 0.000596502 a 0.29217 tau1 24.8856 tau2 443.641
Warning: tau2 is longer than the length of the data (864000)
the st
On 2/02/2012 2:08 AM, aiswarya pawar wrote:
If i give command as =
g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8
this prints out all the protein water distance within 0.8nm. The data printed
out is such that=
t: 1466 5369 SOL 20624 OW 0.789894 (nm)
t: 1467 5369 SOL 20624 OW 0.781596 (
aiswarya pawar wrote:
If i give command as =
g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8
this prints out all the protein water distance within 0.8nm. The data printed
out is such that=
t: 1466 5369 SOL 20624 OW 0.789894 (nm)
t: 1467 5369 SOL 20624 OW 0.781596 (nm)
t: 1469 5369 SO
If i give command as =
g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8
this prints out all the protein water distance within 0.8nm. The data printed
out is such that=
t: 1466 5369 SOL 20624 OW 0.789894 (nm)
t: 1467 5369 SOL 20624 OW 0.781596 (nm)
t: 1469 5369 SOL 20624 OW 0.785377 (nm)
aiswarya pawar wrote:
Hi,
I have used the command =
g_dist -f md.xtc -s md.tpr -n index.ndx
which gives an output of data=
0.0000.62590240.3880.3610001 -0.3329997
1.0000.67787750.25900030.593 -0.198
2.0000.67590300.2529998
On 2/02/2012 12:28 AM, aiswarya pawar wrote:
Hi,
I have used the command =
g_dist -f md.xtc -s md.tpr -n index.ndx
which gives an output of data=
0.0000.62590240.3880.3610001 -0.3329997
1.0000.67787750.25900030.593 -0.198
2.0000.
Hi,
I have used the command =
g_dist -f md.xtc -s md.tpr -n index.ndx
which gives an output of data=
0.0000.62590240.3880.3610001 -0.3329997
1.0000.67787750.25900030.593 -0.198
2.0000.67590300.25299980.593 -0.203
aiswarya pawar wrote:
Dear Gromacs Users,
i have data for the distance between the protein and water atoms within
a cut off of 8A for 5ns using the g_dist option. Now i want to use
g_analyze on this data. The time frame in the output data is not
continuous because of the cut off provided. S
Dear Gromacs Users,
i have data for the distance between the protein and water atoms within a
cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze
on this data. The time frame in the output data is not continuous because
of the cut off provided. So i would like to know how wo
Dear all
I used g_analyze -f dist.xvg -ee
In the one of the my output files, I encountered
Read 1 sets of 1252 points, dt = 0.0119951
std. dev.relative deviation of
standard - cumulants from those of
set
On 30/12/2011 1:06 AM, leila karami wrote:
Dear gromacs users
I want to calculate error estimates using block averaging for output
from g-dist
(distance between donor atom of protein and acceptor atom of dna).
I used g_analyze -f dist.xvg -ee
there are 3 columns in output file.
anyone give
Dear gromacs users
I want to calculate error estimates using block averaging for output from
g-dist
(distance between donor atom of protein and acceptor atom of dna).
I used g_analyze -f dist.xvg -ee
there are 3 columns in output file.
anyone give me more explain about these columns?
how to e
Dear all,
I run a NPT equilibration (1 ns - 1000 steps) and then I drew pressure graph
using g_energy.
I've tried to run the following command
g_analyze -f pressure.xvg -av average.xvg -ee errest.xvg
G_ANALYZE PRESSURE***
But I get the following output
Read 1 s
users-boun...@gromacs.org] On
Behalf Of aiswarya pawar
Sent: Tuesday, 27 September 2011 3:11 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_analyze doubt
Mark,
i read the help but i still didnt understand how do i compute the time series
for this data, should i use this data a
Mark,
i read the help but i still didnt understand how do i compute the time
series for this data, should i use this data as such for the input?
Thanks,
On Mon, Sep 26, 2011 at 12:44 PM, Mark Abraham wrote:
> On 26/09/2011 5:10 PM, aiswarya pawar wrote:
>
>> HI Mark,
>>
>> i have a .xvg data fo
On 26/09/2011 5:10 PM, aiswarya pawar wrote:
HI Mark,
i have a .xvg data for the distance of two atoms in each time frame.
0.00e+00 7.191033e-01
1.00e+00 7.304224e-01
2.00e+00 8.983867e-01
3.00e+00 8.779736e-01
4.00e+00 8.236583e-01
5.00e+00 8.298320e-01
6.00e
HI Mark,
i have a .xvg data for the distance of two atoms in each time frame.
0.00e+00 7.191033e-01
1.00e+00 7.304224e-01
2.00e+00 8.983867e-01
3.00e+00 8.779736e-01
4.00e+00 8.236583e-01
5.00e+00 8.298320e-01
6.00e+00 7.703011e-01
7.00e+00 8.569826e-01
8.
On 26/09/2011 4:51 PM, aiswarya pawar wrote:
Hi users,
I have data with the time frame and the distances, how will compute
the autocorrelation of this. i did g_analyze but still dont understand
what should be the y axis data when providing input for g_analyze.
please help.
I don't understan
Hi users,
I have data with the time frame and the distances, how will compute the
autocorrelation of this. i did g_analyze but still dont understand what
should be the y axis data when providing input for g_analyze. please help.
Thanks
--
gmx-users mailing listgmx-users@gromacs.org
http://li
Hi users,
I have got a data from g_mindist ie water and protein atom distance in each
time frame. Now I have to find the auto correlation function using g_analyze
but my output file from g_mindist has the time frame,water molecule number. How
do I compute the ACF. In ACF data set the x axis is
Thanks a lot for the clarification, now it works perfectly. Sorry for the
confusion!
Best wishes,
Rebeca.
> Date: Fri, 14 Jan 2011 13:46:26 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] g_analyze with multiple sets
>
>
>
> Reb
Rebeca García Fandiño wrote:
Hello,
I have several files containing two columns, x and y (x is the same for
all of them).
I would like to calculate the average and standar deviation (as the
error bar) for the y column for all my data sets.
I have tried using g_analyze:
g_analyze -n 3 -av av
Hello,
I have several files containing two columns, x and y (x is the same for all of
them).
I would like to calculate the average and standar deviation (as the error bar)
for the y column for all my data sets.
I have tried using g_analyze:
g_analyze -n 3 -av average.xvg -errbar stddev -f set1.
s.org
Subject: [gmx-users] g_analyze
In manual g_analyze reads an ascii file and analyzes data sets, in which
input file was graph.xvg. To generate eigenvector and eigenvalue file I
have used g_covar and analyzed eigenvectors by g_aneig. So according to
manual input file should be an ascii file,
In manual g_analyze reads an ascii file and analyzes data sets, in which
input file was graph.xvg. To generate eigenvector and eigenvalue file I have
used g_covar and analyzed eigenvectors by g_aneig. So according to manual
input file should be an ascii file, is it covar.dat file generated by
g_cov
Hello gmx-users,
I am attempting to use g_analyze to find the error estimate on the average
volume of my system. Using an .xvg file with my volume data and the -ee flag I
receive the following message.
Found only 1 number on line, assuming no time is present.
Read 1 sets of 611700 points, dt
extremely long, or does your input have even longer times?
Berk
> From: maximilian.andr...@tu-dortmund.de
> To: gmx-users@gromacs.org
> Date: Mon, 1 Feb 2010 19:49:17 +0100
> Subject: [gmx-users] g_analyze - negative parameters
>
> Dear Gromacs-Users,
>
> I'
Dear Gromacs-Users,
I've been trying to figure out g_analyze for a while now (having read
the manual references and papers), but I still haven't found out what
a negative parameter obtained during fitting means. It's clear that
when Tau2 is longer than the total simulation time the sampling is
bad
A Heddell wrote:
Hi,
I am trying to analyse the number of hydrogen bonds between two sets of
residues in four different structures. I have run g_hbond for the two sets
on each structure and now I wish to work out the average and standard
deviation of the number of hydrogen bonds between these t
Hi,
I am trying to analyse the number of hydrogen bonds between two sets of
residues in four different structures. I have run g_hbond for the two sets
on each structure and now I wish to work out the average and standard
deviation of the number of hydrogen bonds between these two sets for each
s
41 matches
Mail list logo
