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
wrote:
> 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? ru
- Original Message -
From: pawan raghav
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,
Fitting is commonly done mass weighted if the reference file contains
masses, like a run input file. But covariance analysis is only
performed mass weighted if explicitly requested (and masses are
available). If mass-weighted analysis is not requested, the masses for
the fit will all be set to
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 wrote:
> Dear users,
>
> I was using g_covar (gmx 4.5.3) to find the eigenvalue and
> eigenvectors. When I used f
Thanks Sir,
Thanks just now I figured it out!
With regards
kavya
On Wed, Jun 1, 2011 at 6:20 PM, Tsjerk Wassenaar wrote:
> 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 2:4
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
> c
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
> str
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
> 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
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 refere
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 n
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.
YourSourceCode/gromacs/src/tools/
If in Linux OS, try
locate g_covar.c
p.s 4.0.3 is not the latest version. why do not try the latest version?
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Carla Jamous [carlajam...@gmail.co
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?
Ma
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 calcula
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 to
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
___
gmx-user
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
___
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 wi
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 stil
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 with that will be something as calculating the
> 'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoti
by projecting the trajectory onto
> 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 -
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,
>
results 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-u
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
> To: gmx-users@gromacs.org
>
> Hi Vijaya,
>
> >
,
Tsjerk
On Thu, Mar 18, 2010 at 9:11 PM, vijaya subramanian
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
>&
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 t
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
y
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, 2
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
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
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
esday, 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&
- Original Message -
From: Sebastian Breuers
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'
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 wrote:
> Dear All,
>
> I would like to get information on how g_covar calculates the average
> structure file (average.pdb)
>
> My aim was actuall
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?
Th
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" wrote:
Dear GMX users,
I want to calculate the correlated motion between atoms during the md simulation
for that purpose I am using
Hi,
Thanks for your suggestion.
While running the g_covar it is showing the error that aminoacids.dat is not
found, so i have copied the residuetypes.dat(which i seems the new modified
name for aminoacids.dat in current GROMACS version), then it prompts to
choose the group for least square fit, whi
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
HI
Thanks a lot Sir.
On Mon, Feb 21, 2011 at 15:26, Tsjerk Wassenaar 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
> ACE
> AIB
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).
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