Dear All,
I would like to get information on how g_covar calculates the average
structure file (average.pdb)
My aim was actually to get a covariance matrix (deltaR*deltaR) so I
started off by writing my own code, I use MDAnalysis package, so I give psf
and traj files as an input and I generate
Hi Deniz,
The option -ref/-noref is not what you think it is. You want to use -nofit.
Cheers,
Tsjerk
On Fri, Sep 20, 2013 at 2:26 PM, Deniz Aydin denizay...@ku.edu.tr wrote:
Dear All,
I would like to get information on how g_covar calculates the average
structure file (average.pdb)
My
Hello,
I am interested in dynamical analysis of my protein. In the manual, it says
-ascii generates a file that includes the whole covariance matrix, and -xpma
writes the atomic covariance matrix per pair of atoms. I was wondering if
there is a way to have this atomic covariaces in the .dat file
Dear Gromacs users,
I want to calculate the covariance matrix of the center of
mass coordinates of non standard residues. Since I want to
do it mass weighted I need to give the center of mass
masses. From which file does g_covar read the masses?
Thanks a lot
Sebastian
--
gmx-users mailing
On 4/15/13 5:17 AM, Sebastian Waltz wrote:
Dear Gromacs users,
I want to calculate the covariance matrix of the center of
mass coordinates of non standard residues. Since I want to
do it mass weighted I need to give the center of mass
masses. From which file does g_covar read the masses?
Respected Sir / Madam
i did temperature study for that i
need analysis principal component analysis so, i followed GROMACS
Introductory Tutorial (4.5.5)
*g_covar*
g_covar -s md_0_2.tpr -f md_merged_20_ns.xtc -o 2KW8_275_eigenval.xvg -v
2KW8_275_eigenvect.trr
Hi all,
I have a couple of questions regarding g_covar:
First, is there anyway to specify that the covar.dat output will be in R
distance (meaning sqrt(x^2+y^2+Z^2)) and not in separate Cartesian
coordinates? also when examining the output I don't understand how the main
diagonal values are
Hi Gideon,
First, is there anyway to specify that the covar.dat output will be in R
distance (meaning sqrt(x^2+y^2+Z^2)) and not in separate Cartesian
coordinates? also when examining the output I don't understand how the main
diagonal values are different than 1, for instance the x1x1
Hi.
Second, Say I would like to analyze the main difference between two
trajectories of the same protein using PCA. is it KOSHER to use the same
first frame which is identical between both runs as the reference strucutre
and then just append both runs into a single trajectory and then use
Hi,
This questuion may be hard. You need rabbi's advice))
But there are some feature of the reference structure that makes it good or
bad. It is mean deviation of the atomic coordinates of the fited structures
from the reference, the best reference minimizes this measure. For a rigid
I know, but the best reference is mean. And it is another mean that
calculated after fit at some frame.
2011/8/16 Tsjerk Wassenaar tsje...@gmail.com
Hi,
This questuion may be hard. You need rabbi's advice))
But there are some feature of the reference structure that makes it good
or
bad.
Hey Yuri,
What do you mean with mean? Mean without fitting is a single point.
Mean only makes sense after aligning. Now there's a nice recursive
problem:
1. Calculate mean to get reference
2. Align to reference to calculate mean
(http://xkcd.com/754/)
But think about it... aligning to some
Hi Tsjerk.
What do you mean with mean? Mean without fitting is a single point.
Mean only makes sense after aligning. Now there's a nice recursive
problem:
1. Calculate mean to get reference
2. Align to reference to calculate mean
I mean the limit of this sequence is mean) Because it is
Dear all,
Is there a trick to get the numbers for g_covar -xmpa?
If not how can i calculate -xmpa results from -xpm -ascii results?
Thanks
Nihal
--
Elif Nihal Korkmaz
Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui Thomas Record Labs
1101 University Ave, Rm. 8359
Hi,
I am doing Dihedral PCA and followed the steps as mentioned in the Gromacs
documentation http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA
Below are the commands i used:
1) I generated index file for chosen dihedral angles.
2) g_angle -f 100ns_noPBC.xtc -n dangle.ndx -or
Poojari, Chetan wrote:
Hi,
I am doing Dihedral PCA and followed the steps as mentioned in the Gromacs
documentation http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA
Below are the commands i used:
1) I generated index file for chosen dihedral angles.
2) g_angle -f 100ns_noPBC.xtc
Hi All
I have used g_covar to produce a covariance analysis of a trajectory file
and am unsure of the eigenvalues produced.
I expected the numbers to start small (first six almost zero) and increase
as when I used g_nmeig on the Hessian; however, I get the opposite:
# This file was created
# by
Dear users,
I was using g_covar (gmx 4.5.3) to find the eigenvalue and
eigenvectors. When I used for protein which is actually - 3740 in
number, it gave a total of 11220 eigenvalues, similarly for bacbone,
c-alpha atoms, the number of eigenvalues given was not matching
with the number of
Hi Kavya,
Each atom has three coordinates; 3*3740=11220 coordinates, yielding as
many eigenvalues and -vectors.
Cheers,
Tsjerk
On Wed, Jun 1, 2011 at 2:44 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I was using g_covar (gmx 4.5.3) to find the eigenvalue and
eigenvectors.
Thanks Sir,
Thanks just now I figured it out!
With regards
kavya
On Wed, Jun 1, 2011 at 6:20 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Kavya,
Each atom has three coordinates; 3*3740=11220 coordinates, yielding as
many eigenvalues and -vectors.
Cheers,
Tsjerk
On Wed, Jun 1,
Hi Bipin,
The file residuetypes.dat is quite different from aminoacids.dat. You
can paste the following into that file (first line is number of
entries, followed by so many residue names):
49
ABU
ACE
AIB
ALA
ARG
ARGN
ASN
ASN1
ASP
ASP1
ASPH
CYS
CYS1
CYS2
CYSH
DALA
GLN
GLU
GLUH
GLY
HIS
HIS1
Thanks a lot Sir.
On Mon, Feb 21, 2011 at 15:26, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Bipin,
The file residuetypes.dat is quite different from aminoacids.dat. You
can paste the following into that file (first line is number of
entries, followed by so many residue names):
49
ABU
Dear GMX users,
I want to calculate the correlated motion between atoms during the md simulation
for that purpose I am using g_covar(the one which is available under
http://www.gromacs.org/Downloads/User_contributions/Other_software)
but it is not compatible with the GROMACS-4.5.3, so please
Hi Bipin,
Try using a .gro or .pdb file as reference structure (-s). Only .tpr files
are version specific.
Cheers,
Tsjerk
On Feb 21, 2011 8:05 AM, bipin singh bipinel...@gmail.com wrote:
Dear GMX users,
I want to calculate the correlated motion between atoms during the md simulation
for that
Thank you justin and his colleagues and you Mr Tsjerk.
--
sh-karbalaee
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Please search the archive at
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Dear Justin
Hi,I want to use PCA for compare fluctuations two peptides with 13
aa. I use this command g_covar
g_covar #NAME? run2.tpr#NAME? run2.xtc#NAME?
eigenvaluesbackbone.xvg #NAME? eigenvectorsbackbone.trr#NAME?
covarbackbon.xpm
and get the some of data :
Hi Karbalee,
It says : nanometer squared.
Cheers,
Tsjerk
PS. Many of us are not Justin... :p
On Sat, Jan 15, 2011 at 5:33 PM, shahrbanoo karbalaee
shahrba...@gmail.com wrote:
Dear Justin
Hi,I want to use PCA for compare fluctuations two peptides with 13
aa. I use this command g_covar
Date: Tuesday, September 7, 2010 0:42
Subject: Re: [gmx-users] g_covar g_anaeig problems
To: gmx-users@gromacs.org
Hey everyone,
searching the list for the answer to a g_covar problem I've
found this post of Arne who describes the very same problem that
I encounter.
I'm observing this problem
- Original Message -
From: Sebastian Breuers breue...@uni-koeln.de
Date: Tuesday, September 7, 2010 17:47
Subject: Re: [gmx-users] g_covar g_anaeig problems
To: gmx-users@gromacs.org
Hey,
taking fewer atoms by ignoring the hydrogens is a good advice.
Thanks a lot.
That's just
Hey everyone,
searching the list for the answer to a g_covar problem I've found this
post of Arne who describes the very same problem that I encounter.
I'm observing this problem on a linux cluster with 32GB memory on each
node. The g_covar_d application was compiled in double precision with
- Original Message -
From: Sebastian Breuers breue...@uni-koeln.de
Date: Tuesday, September 7, 2010 0:42
Subject: Re: [gmx-users] g_covar g_anaeig problems
To: gmx-users@gromacs.org
Hey everyone,
searching the list for the answer to a g_covar problem I've
found this post of Arne
Hi everyone,
please I'm using gromacs 4.0.3, and I want to see the program g_covar,
except that I have it in binary file and I want to see the C program in text
format.
Please how can I have access to it?
Thank you
Carla
--
gmx-users mailing listgmx-users@gromacs.org
Carla Jamous wrote:
Hi everyone,
please I'm using gromacs 4.0.3, and I want to see the program g_covar,
except that I have it in binary file and I want to see the C program in
text format.
Please how can I have access to it?
Download the source code, then look at src/tools/gmx_covar.c.
...@gmail.com]
Sent: Monday, August 30, 2010 8:53 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] g_covar
Hi everyone,
please I'm using gromacs 4.0.3, and I want to see the program g_covar, except
that I have it in binary file and I want to see the C program in text format.
Please how can I
Thanks Mark for your advice
Note: The fit analysis group are identical, while the fit is mass weighted
and the analysis is not making the fit non mass weighted.
But, this is the the real unning out put of the command prompt
Please let me know anyone what is the meaning of this note? and also
- Original Message -
From: pawan raghav pwnr...@gmail.com
Date: Wednesday, June 2, 2010 4:18
Subject: [gmx-users] g_covar
To: gmx-users@gromacs.org
Thanks Mark for your advice Note: The fit analysis group are identical,
while the fit is mass weighted and the analysis
:
- Original Message -
From: pawan raghav pwnr...@gmail.com
Date: Wednesday, June 2, 2010 4:18
Subject: [gmx-users] g_covar
To: gmx-users@gromacs.org
Thanks Mark for your advice
Note: The fit analysis group are identical, while the fit is mass weighted
and the analysis is not making the fit non
Hi Jared,
Can you post the exact series of commands you used to come to this
point, including the selections you used and what constitutes these
selections if they are not standard? Please also indicate what was in
the trajectory you started off with (xtc-grps).
Cheers,
Tsjerk
On Thu, Mar 25,
Hi everyone,
I've got the following two problems - hopefully someone can help me
fixing them.
1.:
I have a larger system ~2 atoms where I performed an MD run and
now I want to analyze the entropy. I tried a combination of g_covar
and g_anaeig to get the values.
Input:
g_covar -f XXX_md_eq.xtc
Greetings,
I'm trying to use g_covar to generate a covariance matrix, followed by g_anaeig
to analyze the data. The trajectory is a list of clusters generated by g_cluster
in .trr format. gmxcheck seems to think that the input trajectory is fine but
the cluster trajectory gives this error when
Hi
Has anyone studied the effect of using different reference structures,
not the average structure, when carrying out PCA. Does it make sense to use
a structure besides the average to calculate the covariance matrix?
Thanks
Vijaya
Hi
Does anyone studied the effect of using different reference structures,
not the average structure, when carrying out PCA. Does it make sense to use
a structure besides the average to calculate the covariance matrix?
Thanks
Vijaya
Hi Vijaya,
Well, to start with that will be something as calculating the
'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith
atom of the conformation x and the reference structure r and the sum
is over time/observations. In the case of no variation in xi, the
value you get will
, 18 Mar 2010 17:51:04 +0100
Subject: Re: [gmx-users] g_covar -ref
From: tsje...@gmail.com
To: gmx-users@gromacs.org
Hi Vijaya,
Well, to start with that will be something as calculating the
'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith
atom of the conformation x
the eigenvectors of the covariance matrix.
I just wanted to know why the option -ref was offered and if it had any
significance.
Thanks
Vijaya
Date: Thu, 18 Mar 2010 17:51:04 +0100
Subject: Re: [gmx-users] g_covar -ref
From: tsje...@gmail.com
To: gmx-users@gromacs.org
Hi Vijaya,
Well, to start
Hi
Your answer truly eludes me, unless -ref is an useless option.
In any case it isn't particularly important.
Vijaya
Date: Thu, 18 Mar 2010 19:37:40 +0100
Subject: Re: [gmx-users] g_covar -ref
From: tsje...@gmail.com
To: gmx-users@gromacs.org
Hi Vijaya,
I'm sorry if I didn't quite
then mean? This is a neat
example to run with pen and paper... You should even be able to solve
it analytically :)
Have fun,
Tsjerk
In any case it isn't particularly important.
Vijaya
Date: Thu, 18 Mar 2010 19:37:40 +0100
Subject: Re: [gmx-users] g_covar -ref
From: tsje...@gmail.com
To: gmx
,
Tsjerk
On Thu, Mar 18, 2010 at 9:11 PM, vijaya subramanian
vijay...@hotmail.com wrote:
Hi
Thanks for your input, what are the few specific cases where
a reference structure might be used?
Vijaya
Date: Thu, 18 Mar 2010 20:42:36 +0100
Subject: Re: [gmx-users] g_covar -ref
From: tsje...@gmail.com
Hello everybody,
in an attempt to calculate the free-energy surface of a peptide, i
followed exactly the procedure described in
http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA
except that g_angle seems to need no -s option in my gromacs
version(4.0.5).
Everything goes fine till the
Peyman Yamin wrote:
Hello everybody,
in an attempt to calculate the free-energy surface of a peptide, i
followed exactly the procedure described in
http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA
except that g_angle seems to need no -s option in my gromacs
version(4.0.5).
You
Hi ALL,
I have a system of beads with which I ran a CGMD (coarse grained MD) using
NAMD. Now I want to do a PCA analysis of this system using GROMACS. So I
converted the trajectory in .trr format and made an index file of the entire
system (45 beads). But now when I try to run g_covar using
Anirban Ghosh wrote:
Hi ALL,
I have a system of beads with which I ran a CGMD (coarse grained MD)
using NAMD. Now I want to do a PCA analysis of this system using
GROMACS. So I converted the trajectory in .trr format and made an index
file of the entire system (45 beads). But now when I try
Anirban Ghosh a écrit :
Hi ALL,
I have a system of beads with which I ran a CGMD (coarse grained MD)
using NAMD. Now I want to do a PCA analysis of this system using
GROMACS. So I converted the trajectory in .trr format
Convert a dcd file into a trr file is not that straightforward. How did
Dear GMX users,
I've uploaded a version of g_covar that can be used to calculate the
correlation of motion between atoms to the user contributions. I hope
some of you would find it useful.
Ran
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Mark Abraham wrote:
tangxuan wrote:
Thanks for your reply. I have another question. I can get the
coordinates covariance by option -ascii, but do you know how to get a
exact covariance value for each atom?
How do you mean exact, and in what format?
Mark
tangxuan wrote:
Mark Abraham wrote:
tangxuan wrote:
Thanks for your reply. I have another question. I can get the
coordinates covariance by option -ascii, but do you know how to get a
exact covariance value for each atom?
How do you mean exact, and in what format?
Mark
Mark Abraham wrote:
tangxuan wrote:
Mark Abraham wrote:
tangxuan wrote:
Thanks for your reply. I have another question. I can get the
coordinates covariance by option -ascii, but do you know how to get
a exact covariance value for each atom?
How do you mean exact, and in what format?
Dear all,
When I am using g_covar to calculate the covariance matrix for alpha
carbons in one subunit of my protein, I get a warning WARNING number of
atoms in tpx (929) and trajectory (293401) do not match. 929 is the
alpha carbon number and 293401 is whole system atom number. In the
This is an incorrect warning, which has been introduced in
version 3.3.2. I have corrected the warning for 3.3.3.
Berk.
Date: Wed, 9 Jan 2008 14:51:52 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] g_covar
Dear all,
When I am using g_covar to calculate
Berk Hess wrote:
This is an incorrect warning, which has been introduced in
version 3.3.2. I have corrected the warning for 3.3.3.
Berk.
Date: Wed, 9 Jan 2008 14:51:52 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] g_covar
Dear all,
When I am using g_covar
tangxuan wrote:
Thanks for your reply. I have another question. I can get the
coordinates covariance by option -ascii, but do you know how to get a
exact covariance value for each atom?
How do you mean exact, and in what format?
Mark
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