Re: [gmx-users] g_covar average.pdb calculation

[Tsjerk Wassenaar]

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 actually to get a covariance matrix () 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 the coordinates for each frame,
> and if I have 3 frames, I take the average of each coordinate element for 3
> frames. So for the 1st CA atom, I have x, y, z values for 3 frames. So I
> add
> x1, x2, x3 values and divide by the number of frames. So this gives me the
> average x coordinate of the 1st CA atom. I do the same for y and z and then
> for all CA atoms. So if x1, x2, x3 for CA1 is 49.5 49.0 and 49.4 for 3
> frames, the average x i get is 49.3. This is what I call an average
> structure.
>
> After doing this, I wanted to compare this with what g_covar gives me
> (average.pdb) but found out that the result that I get from my own
> calculations and the result I get from g_covar are very very different. The
> g_covar command that I use is the following:
>
> g_covar -f traj.xtc -s topol.tpr -ascii covar.dat -xpm covar.xpm -noref
>
> Here I use -noref because I already use trjconv on my initial trajectory to
> generate a new trajectory so I do -pbc mol and center and -fit rot+trans to
> remove translation, rotation and to fit the structure. So I thought I could
> use -nofit in g_covar to not to fit to the reference structure again.
>
> So, coming back to my question, why would g_covar give me a very different
> result than what I find with my simple code? What does g_covar do to
> calculate this average structure? I thought maybe it does some fitting or
> additional stuff to what I'm doing in my code or changes the units, that in
> the end it doesn't give me the same coordinates for the average.pdb.
>
> -
> Deniz Aydin, BSc.
> Graduate Student
>
> Chemical & Biological Engineering
> Graduate School of Sciences and Engineering
> Koç University, Istanbul, Turkey
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/g-covar-average-pdb-calculation-tp5011339.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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RE: [gmx-users] g_covar -ascii

[Payman Pirzadeh]

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 with -ascii
switch. Otherwise, is there a script in gromacs that converts the xpm to an
ascii file? In addition, is the -xpma output normalized?
Thanks for your help.

Payman 


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Re: [gmx-users] g_covar with individual masses

[Justin Lemkul]

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?



The only file g_covar reads that stores mass information is the .tpr file.

-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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Re: [gmx-users] g_covar

[Yuri Garmay]

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 naturally enough to
mean that mean is value that minimizes deviation.
And I know (I learned this a few days ago, in my calculations) that for
flexible molecules such as short peptides it is very another mean that
calculated after first fit. Moreover, if molecule flexible enough, fit to
some frame may be unstable (there may be similar structures that fit in non
similar orientation).

Regards,
Yuri.
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Re: [gmx-users] g_covar

[Tsjerk Wassenaar]

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 reference is good enough to fix
the mean and the covariance matrix. :)

Cheers,

Tsjerk

On Tue, Aug 16, 2011 at 11:16 AM, Yuri Garmay  wrote:
> 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 mean deviation of the atomic coordinates of the fited
>> > structures
>> > from the reference, the best reference minimizes this measure. For a
>> > rigid
>> > structure it is acceptable choice to use first or any other frame, but
>> > for a
>> > flexible it can produce misfit and tangible distortion of the
>> > conformations'
>> > relations.
>>
>> The reference is used to align the system, not to calculate the
>> deviations, unless explicitly specified to do so, which usually does
>> not make sense. I've commented on that on the list on several
>> occasions. Taking the first frame, or the last or another is all fine.
>> Just as long as the same reference is used for all trajectories that
>> are to be compared.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> >
>> > Yuri.
>> >
>> > --
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>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
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-- 
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] g_covar

[Yuri Garmay]

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 mean deviation of the atomic coordinates of the fited
> structures
> > from the reference, the best reference minimizes this measure. For a
> rigid
> > structure it is acceptable choice to use first or any other frame, but
> for a
> > flexible it can produce misfit and tangible distortion of the
> conformations'
> > relations.
>
> The reference is used to align the system, not to calculate the
> deviations, unless explicitly specified to do so, which usually does
> not make sense. I've commented on that on the list on several
> occasions. Taking the first frame, or the last or another is all fine.
> Just as long as the same reference is used for all trajectories that
> are to be compared.
>
> Cheers,
>
> Tsjerk
>
> >
> > Yuri.
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
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Re: [gmx-users] g_covar

[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 mean deviation of the atomic coordinates of the fited structures
> from the reference, the best reference minimizes this measure. For a rigid
> structure it is acceptable choice to use first or any other frame, but for a
> flexible it can produce misfit and tangible distortion of the conformations'
> relations.

The reference is used to align the system, not to calculate the
deviations, unless explicitly specified to do so, which usually does
not make sense. I've commented on that on the list on several
occasions. Taking the first frame, or the last or another is all fine.
Just as long as the same reference is used for all trajectories that
are to be compared.

Cheers,

Tsjerk

>
> Yuri.
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] g_covar

[Yuri Garmay]

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 g_covar
> to analyse the subsequent conformations? if not, how would one go about
> comparing the PC's of two different trajectories? other than dumping all the
> frames in gro/pdb format and running the analysis in another program (such
> as MATLAB)
>
>
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
structure it is acceptable choice to use first or any other frame, but for a
flexible it can produce misfit and tangible distortion of the conformations'
relations.


Yuri.
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Re: [gmx-users] g_covar

[Tsjerk Wassenaar]

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
> covariance should be 1.. or am I missing something?

No, that is quite a different thing. But g_rms -rmsdist does just that :)
Then, the diagonal entries are variances/fluctuations, not
self-correlations, which are unity by definition.

> 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 g_covar
> to analyse the subsequent conformations? if not, how would one go about
> comparing the PC's of two different trajectories? other than dumping all the
> frames in gro/pdb format and running the analysis in another program (such
> as MATLAB)

Fitting all to the same reference is fine. Then calculating the
principal components on the concatenated trajectory is what is
sometimes called 'combined essential dynamics'. But it's not good for
comparing principal components. It will give one set of components for
all frames and allows you to compare the projections of the separate
trajectories onto these components, from which you can infer in how
far they sample the same or different subspaces. To compare the
eigenvectors, you need to calculate components on the separate
trajectories, fitting each onto the same reference. The sets of
principal components can then be used to calculate the overlap between
the subspaces sampled. Check the manpage for g_anaeig.

Hope it helps,

Tsjerk

>
> Thanks,
>
> Gideon
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-- 
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] g_covar : segmentation fault

[Justin A. Lemkul]

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 -n dangle.ndx -or dangle.trr -type dihedral

3) trjconv -s md_100ns.tpr -f dangle.trr -o resized.gro -n covar.ndx -e 0

4) g_covar -f dangle.trr -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc 
-s resized.gro


While running the command in step 4, it runs for sometime and then i get 
segmentation fault. I was doing these in Gromacs 4.5.4 package.


When i switched to Gromacs 4.0.7 package and repeated the steps, i ran 
successfully without any errors.

Please can I know what changes can be done to the commands I have used so that 
i can get it running with Gromacs 4.5.4 package as well.



Typically, when an old version works and the new version is broken, a bug is at 
fault.  If you consistently observe this behavior with other systems or smaller 
systems (to rule out simply running out of memory, etc), then please file a bug 
report on redmine.gromacs.org with all necessary input files to reproduce the 
problem.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] g_covar

[Kavyashree M]

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 2:44 PM, Kavyashree M  wrote:
> > Dear users,
> >
> >  I was using g_covar (gmx 4.5.3) to find the eigenvalue and
> > eigenvectors. When I used 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 atoms in question.
> > I presume that the number of eigenvalues generated should correspond
> > to the number of atoms considered in question.
> > But the xpm file generated corresponds with the query given ie., protein,
> > C-alpha or backbone as expected.
> >
> > Kindly clarify my doubts.
> >
> > Thank you
> > With regards
> > M. Kavyashree
> >
> > --
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
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Re: [gmx-users] g_covar

[Tsjerk Wassenaar]

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 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 atoms in question.
> I presume that the number of eigenvalues generated should correspond
> to the number of atoms considered in question.
> But the xpm file generated corresponds with the query given ie., protein,
> C-alpha or backbone as expected.
>
> Kindly clarify my doubts.
>
> Thank you
> With regards
> M. Kavyashree
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] g_covar to calculate correlation of motion

[bipin singh]

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
> ALA
> ARG
> ARGN
> ASN
> ASN1
> ASP
> ASP1
> ASPH
> CYS
> CYS1
> CYS2
> CYSH
> DALA
> GLN
> GLU
> GLUH
> GLY
> HIS
> HIS1
> HISA
> HISB
> HISH
> HYP
> ILE
> LEU
> LYS
> LYSH
> MELEU
> MET
> MEVAL
> NAC
> NH2
> PHE
> PHEH
> PHEU
> PHL
> PRO
> SER
> THR
> TRP
> TRPH
> TRPU
> TYR
> TYRH
> TYRU
> VAL
>
>
> Groetjes,
>
> Tsjerk
>
> On Mon, Feb 21, 2011 at 8:47 AM, bipin singh  wrote:
> > 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, which is not usual groups(i.e
> protein
> > or C alpha groups etc.).please suggest where i have made mistake.
> >
> > Choose a group for the least squares fit
> > Opening library file aminoacids.dat
> > WARNING 2 [file aminoacids.dat, line 1]:
> >   File aminoacids.dat is empty
> > Group 0 (  System) has 30585 elements
> > Group 1 ( GLU) has47 elements
> > Group 2 ( HIS) has86 elements
> > Group 3 ( ASN) has   224 elements
> > Group 4 ( PRO) has56 elements
> > Group 5 ( VAL) has   272 elements
> > Group 6 ( MET) has68 elements
> > Group 7 ( GLY) has   168 elements
> > Group 8 ( ILE) has   190 elements
> > Group 9 ( ALA) has   110 elements
> > Group10 ( SER) has   143 elements
> > Group11 ( PHE) has80 elements
> > Group12 ( LYS) has   242 elements
> > Group13 ( TYR) has   189 elements
> > Group14 ( LEU) has   304 elements
> > Group15 ( GLN) has   102 elements
> > Group16 ( TRP) has48 elements
> > Group17 ( ARG) has   120 elements
> > Group18 ( ASP) has   108 elements
> > Group19 ( THR) has   141 elements
> > Group20 ( SOL) has 27882 elements
> > Group21 (  CL) has 5 elements
> >
> >
> > On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar 
> wrote:
> >>
> >> 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 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 suggest me
> the
> >> alternative way or does anyone have the modified g_covar for
> >> GROMKACS-4.5.3.
> >>
> >> --
> >> -
> >> Thanks and regards
> >> Bipin Singh
> >>
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
> >
> > --
> > -
> > Thanks and regards
> > Bipin Singh
> >
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search 

Re: [gmx-users] g_covar to calculate correlation of motion

[Tsjerk Wassenaar]

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
HISA
HISB
HISH
HYP
ILE
LEU
LYS
LYSH
MELEU
MET
MEVAL
NAC
NH2
PHE
PHEH
PHEU
PHL
PRO
SER
THR
TRP
TRPH
TRPU
TYR
TYRH
TYRU
VAL


Groetjes,

Tsjerk

On Mon, Feb 21, 2011 at 8:47 AM, bipin singh  wrote:
> 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, which is not usual groups(i.e protein
> or C alpha groups etc.).please suggest where i have made mistake.
>
> Choose a group for the least squares fit
> Opening library file aminoacids.dat
> WARNING 2 [file aminoacids.dat, line 1]:
>   File aminoacids.dat is empty
> Group 0 (  System) has 30585 elements
> Group 1 ( GLU) has    47 elements
> Group 2 ( HIS) has    86 elements
> Group 3 ( ASN) has   224 elements
> Group 4 ( PRO) has    56 elements
> Group 5 ( VAL) has   272 elements
> Group 6 ( MET) has    68 elements
> Group 7 ( GLY) has   168 elements
> Group 8 ( ILE) has   190 elements
> Group 9 ( ALA) has   110 elements
> Group    10 ( SER) has   143 elements
> Group    11 ( PHE) has    80 elements
> Group    12 ( LYS) has   242 elements
> Group    13 ( TYR) has   189 elements
> Group    14 ( LEU) has   304 elements
> Group    15 ( GLN) has   102 elements
> Group    16 ( TRP) has    48 elements
> Group    17 ( ARG) has   120 elements
> Group    18 ( ASP) has   108 elements
> Group    19 ( THR) has   141 elements
> Group    20 ( SOL) has 27882 elements
> Group    21 (  CL) has 5 elements
>
>
> On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar  wrote:
>>
>> 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 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 suggest me the
>> alternative way or does anyone have the modified g_covar for
>> GROMKACS-4.5.3.
>>
>> --
>> -
>> Thanks and regards
>> Bipin Singh
>>
>>
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
> -
> Thanks and regards
> Bipin Singh
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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Re: [gmx-users] g_covar to calculate correlation of motion

[bipin singh]

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, which is not usual groups(i.e protein
or C alpha groups etc.).please suggest where i have made mistake.

Choose a group for the least squares fit
Opening library file aminoacids.dat
WARNING 2 [file aminoacids.dat, line 1]:
  File aminoacids.dat is empty
Group 0 (  System) has 30585 elements
Group 1 ( GLU) has47 elements
Group 2 ( HIS) has86 elements
Group 3 ( ASN) has   224 elements
Group 4 ( PRO) has56 elements
Group 5 ( VAL) has   272 elements
Group 6 ( MET) has68 elements
Group 7 ( GLY) has   168 elements
Group 8 ( ILE) has   190 elements
Group 9 ( ALA) has   110 elements
Group10 ( SER) has   143 elements
Group11 ( PHE) has80 elements
Group12 ( LYS) has   242 elements
Group13 ( TYR) has   189 elements
Group14 ( LEU) has   304 elements
Group15 ( GLN) has   102 elements
Group16 ( TRP) has48 elements
Group17 ( ARG) has   120 elements
Group18 ( ASP) has   108 elements
Group19 ( THR) has   141 elements
Group20 ( SOL) has 27882 elements
Group21 (  CL) has 5 elements


On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar  wrote:

> 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 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 suggest me the 
> alternative way or does anyone have the modified g_covar for
> GROMKACS-4.5.3.
>
> --
> *
> -
> Thanks and regards
> Bipin Singh
> *
> *
> *
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
*
-
Thanks and regards
Bipin Singh
*
*
*
-- 
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Re: [gmx-users] g_covar to calculate correlation of motion

[Tsjerk Wassenaar]

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 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 suggest me
the alternative way or does anyone have the modified g_covar for
GROMKACS-4.5.3.

-- 
*
-
Thanks and regards
Bipin Singh
*
*
*


--
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Re: [gmx-users] g_covar

[Tsjerk Wassenaar]

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?  run2.tpr        #NAME?  run2.xtc        #NAME?  
> eigenvaluesbackbone.xvg #NAME?  eigenvectorsbackbone.trr        #NAME?  
> covarbackbon.xpm
>
> and get the some of data :  title       Eigenvalues of the covariance matrix
> xaxis   label   Eigenvector index
> yaxis   label   (nm\S2\N)
>
> would you  please tell me about  Yaxis.  What is  meaning of  (nm/s2/n)?
>
> Best
> Karbalaee
>
>
>
> sh-karbalaee
> --
> gmx-users mailing list    gmx-users@gromacs.org
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> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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Re: [gmx-users] g_covar & g_anaeig problems

[Mark Abraham]

- 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's just the tip of the iceberg, of course. Even as little as your C-alpha 
atoms might be sufficient for the purpose.

 
> I was wondering if a more appropriate error message could be 
> generated before the program messes around in the memory. The 
> program acts as if it could handle the system size and then 
> crashes with a Segmentation fault meaning it does not properly 
> handle its memory.

Sure, that would be nice behaviour. Unfortunately the algorithms used for 
diagonalization are called from another library, and GROMACS can't 
realistically anticipate its memory usage. Moreover, finding out from the 
system how much virtual memory is available and from the user whether virtual 
memory use is acceptable is all more work than it's worth. I have added a note 
in the g_covar documentation to clue the user in to how best to manage the 
situation.

Mark

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Re: [gmx-users] g_covar & g_anaeig problems

[Sebastian Breuers]

Hey,

taking fewer atoms by ignoring the hydrogens is a good advice. Thanks a 
lot.


I was wondering if a more appropriate error message could be generated 
before the program messes around in the memory. The program acts as if 
it could handle the system size and then crashes with a Segmentation 
fault meaning it does not properly handle its memory.


Nonetheless thanks again for the hydrogen advice. Had'nt really thought 
about it before.


Kind regards

Sebastian


Am 07.09.2010 03:44, schrieb Mark Abraham:



- 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 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 an intel compiler and works fine up to a number
> of atoms of around 15408. In tests I could find out that above
> this number +/- 48 atoms I receive the following error output:
>
>
> Calculating the average structure ...
> Last frame 50
> time 5000.000
>
> Constructing covariance matrix (46368x46368) ...
> Reading frame   0
> time0.000   Segmentation fault
>
> Meaning a matrix over around 46224x46224 elements starts to
> generate this problem.
>
> Did anyone encounter the same problem or does anyone has a hint
> to solve this issue?

Get more memory or use fewer atoms :-) The memory needs and run time 
will scale at least as high as the square of the number of atoms. 
Probably you can ignore at least your hydrogen atoms...


Mark 



--
_

Sebastian Breuers   Tel: +49-221-470-4108
EMail: breue...@uni-koeln.de

Universität zu Köln University of Cologne
Department für Chemie   Department of Chemistry
Organische Chemie   Organic Chemistry

Greinstraße 4   Greinstraße 4
D-50939 KölnD-50939 Cologne, Federal Rep. of Germany
_

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Re: [gmx-users] g_covar & g_anaeig problems

[Mark Abraham]

- 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 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 an intel compiler and works fine up to a number 
> of atoms of around 15408. In tests I could find out that above 
> this number +/- 48 atoms I receive the following error output:
> 
> 
> Calculating the average structure ...
> Last frame 50 
> time 5000.000
> 
> Constructing covariance matrix (46368x46368) ...
> Reading frame   0 
> time0.000   Segmentation fault
> 
> Meaning a matrix over around 46224x46224 elements starts to 
> generate this problem.
> 
> Did anyone encounter the same problem or does anyone has a hint 
> to solve this issue?

Get more memory or use fewer atoms :-) The memory needs and run time will scale 
at least as high as the square of the number of atoms. Probably you can ignore 
at least your hydrogen atoms...

Mark

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Re: [gmx-users] g_covar & g_anaeig problems

[Sebastian Breuers]

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 an 
intel compiler and works fine up to a number of atoms of around 15408. 
In tests I could find out that above this number +/- 48 atoms I receive 
the following error output:



Calculating the average structure ...
Last frame 50 time 5000.000

Constructing covariance matrix (46368x46368) ...
Reading frame   0 time0.000   Segmentation fault

Meaning a matrix over around 46224x46224 elements starts to generate 
this problem.


Did anyone encounter the same problem or does anyone has a hint to solve 
this issue?


Kind regards

Sebastian



Am 25.03.2010 10:05, schrieb arne.wag...@student.uib.no:

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 -n XXX.ndx -s XXX_md_eq.tpr -v XXX_eivec.trr
-mwa -l XXX_covar.log

If I choose a larger sub-part of the system (approx. > 4000 elements)
I get the following error message after the average structure is
calculated:

Constructing covariance matrix ...
Reading frame   0 time0.000   Segmentation fault

Is this a result of insufficient memory or is there an error in the
whole procedure?

2.:
In smaller sub-parts I can get the eigenvectors and when I put them
into g_anaeig,

g_anaeig -v XXX.trr -entropy

I get values for the quasi-harmonical-approximation but
an 'inf' oder 'nan' for the Schlitter entropy calculation - even with
additional/maximum input. Why?

Thanks a lot!
Awa




--
_

Sebastian Breuers   Tel: +49-221-470-4108
EMail: breue...@uni-koeln.de

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RE: [gmx-users] g_covar

[#ZHAO LINA#]

 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.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 have access to it?

Thank you
Carla
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Re: [gmx-users] g_covar

[Justin A. Lemkul]

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.

-Justin


Thank you
Carla



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] g_covar

[Tsjerk Wassenaar]

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 one, so as to assure that the fit and the
analysis will concern the same thing. That is what the message is
trying to tell. So no problem (unless you wanted mass-weighted
analysis).

Hope it helps,

Tsjerk

On Tue, Jun 1, 2010 at 8:51 PM, Mark Abraham  wrote:
>
>
> - 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 mass weighted.
>>
>> But, this is the the real unning out put of the command prompt
>
> No, it isn't. :-) I've now consulted the 4.0.7 source code, this message
> would have had a full stop and a capital M. Since they were missing, it
> looked like you were saying something confused.
>
> g_covar won't do a mass-weighted fit with a non-mass-weighted analysis.
> g_covar -h talks about this.
>
>> Please let me know anyone what is the meaning of this note? and also tell
>> me is it right to choose C-alpha group for two times?   >
>
>> Yes I want to do the structure-fitting on the same set of atoms as I do
>> the analysis.
>
> Well, then you need to make a choice consistent with that.
>
> Mark
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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Re: [gmx-users] g_covar

[Mark Abraham]

- 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 
> mass weighted. >   > But, this is the the real unning out put of the command 
> prompt

No, it isn't. :-) I've now consulted the 4.0.7 source code, this message would 
have had a full stop and a capital M. Since they were missing, it looked like 
you were saying something confused.

g_covar won't do a mass-weighted fit with a non-mass-weighted analysis. g_covar 
-h talks about this.
 
 > Please let me know anyone what is the meaning of this note? and also tell me 
 > is it right to choose C-alpha group for two times?   > 
> Yes I want to do the structure-fitting on the same set of atoms as I do the 
> analysis.

Well, then you need to make a choice consistent with that.

Mark


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Re: [gmx-users] g_covar & g_anaeig problems

[Tsjerk Wassenaar]

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, 2010 at 10:31 PM, Jared James Thompson
 wrote:
> 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 gmxcheck is used:
>
> Timesteps at t=9974 don't match (2, 4)
>
> Timesteps at t=9978 don't match (4, 2)
>
> for every t += 4.
>
> g_covar crashes when I use my trajectory, giving the message:
>
> WARNING: number of atoms in tpx (730) and trajectory (730) do not match
> and then usually gives a segmentation fault message or a memory error.
>
> Help?
>
> best,
> Jared
>
>
>
>
>
>
> --
> Jared James Thompson
> Department of Medicinal Chemistry and Molecular Pharmacology
> Laboratory for Computational Drug Design and Biology
> RHPH 504C
> Heine Pharmacy Building
> 575 Stadium Mall Drive
> West Lafayette, IN  47907-2091
> --
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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Re: [gmx-users] g_covar -ref

[Tsjerk Wassenaar]

Hi Vijaya,

Hmmm. Well, it may make some sense to take a defined extreme point to
take deviations from. Like for motion on an arc, it may make sense to
take the center of the circle to determine the deviations. But what
that will yield; how that translates to wiggling proteins... :S

Cheers,

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
>> From: tsje...@gmail.com
>> To: gmx-users@gromacs.org
>>
>> Hi Vijaya,
>>
>> > Your answer truly eludes me, unless -ref is an useless option.
>>
>> Well, that's pretty close to the conclusion. The use is limited to a
>> few very specific cases and it might be better to hide the option from
>> the view of casual users.
>>
>> But apparently you didn't catch the why yet. If you imagine a pendulum
>> going back and forth, the principal components will be commonly
>> determined by taking the deviations from the mean position. Then you
>> get two components, one for the direction of the motion and one for
>> the deflection from linearity, right? But now, you calculate the
>> deviations not with respect to the average position, but you take the
>> deviations with respect to a position that is away from the mean, say
>> halfway to the left. Now you can follow the same procedure,
>> calculating a matrix of cross products for these deviations, and
>> diagonalizing it. But what do these 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-users] g_covar -ref
>> >> From: tsje...@gmail.com
>> >> To: gmx-users@gromacs.org
>> >>
>> >> Hi Vijaya,
>> >>
>> >> I'm sorry if I didn't quite get that first sentence of yours. Did you
>> >> meant to start it with "I thought that ..."? Or were you trying to
>> >> explain me something you thought I missed?
>> >>
>> >> PCA stands for 'principal component analysis', not 'covariance
>> >> analysis'. For instance, PCA can be applied to correlations, and then
>> >> is 'correlation analysis'. SVD is a particular flavour of PCA and here
>> >> yields the same results as traditional PCA because the covariance
>> >> matrix is symmetric, but otherwise they're not strictly the same. That
>> >> is to say, the SVD is obtained by extracting the eigenvectors from the
>> >> matrices transpose(S) x S and S x transpose(S). Which are quite
>> >> obviously identical if S is a symmetric matrix.
>> >>
>> >> By the way, was your question regarding the -ref option answered, or
>> >> did the answer elude you? If the latter is the case, maybe if now you
>> >> feel sufficiently confident that I know a bit about PCA, you can go
>> >> through the answer again.
>> >>
>> >> Cheers,
>> >>
>> >> Tsjerk
>> >>
>> >> On Thu, Mar 18, 2010 at 7:01 PM, vijaya subramanian
>> >>  wrote:
>> >> > PCA refers to covariance analysis (though SVD gives the same
>> >> > results).
>> >> > Principal components are obtained 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 -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 and the reference structure r and the sum
>> >> >> is over time/o

RE: [gmx-users] g_covar -ref

[vijaya subramanian]

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,
> 
> > Your answer truly eludes me, unless -ref is an useless option.
> 
> Well, that's pretty close to the conclusion. The use is limited to a
> few very specific cases and it might be better to hide the option from
> the view of casual users.
> 
> But apparently you didn't catch the why yet. If you imagine a pendulum
> going back and forth, the principal components will be commonly
> determined by taking the deviations from the mean position. Then you
> get two components, one for the direction of the motion and one for
> the deflection from linearity, right? But now, you calculate  the
> deviations not with respect to the average position, but you take the
> deviations with respect to a position that is away from the mean, say
> halfway to the left. Now you can follow the same procedure,
> calculating a matrix of cross products for these deviations, and
> diagonalizing it. But what do these 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-users] g_covar -ref
> >> From: tsje...@gmail.com
> >> To: gmx-users@gromacs.org
> >>
> >> Hi Vijaya,
> >>
> >> I'm sorry if I didn't quite get that first sentence of yours. Did you
> >> meant to start it with "I thought that ..."? Or were you trying to
> >> explain me something you thought I missed?
> >>
> >> PCA stands for 'principal component analysis', not 'covariance
> >> analysis'. For instance, PCA can be applied to correlations, and then
> >> is 'correlation analysis'. SVD is a particular flavour of PCA and here
> >> yields the same results as traditional PCA because the covariance
> >> matrix is symmetric, but otherwise they're not strictly the same. That
> >> is to say, the SVD is obtained by extracting the eigenvectors from the
> >> matrices transpose(S) x S and S x transpose(S). Which are quite
> >> obviously identical if S is a symmetric matrix.
> >>
> >> By the way, was your question regarding the -ref option answered, or
> >> did the answer elude you? If the latter is the case, maybe if now you
> >> feel sufficiently confident that I know a bit about PCA, you can go
> >> through the answer again.
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >>
> >> On Thu, Mar 18, 2010 at 7:01 PM, vijaya subramanian
> >>  wrote:
> >> > PCA refers to covariance analysis (though SVD gives the same results).
> >> > Principal components are obtained 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 -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 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 still be finite, in stead of zero, as would
> >> >> probably be most meaningful.
> >> >> Now for the covariances, there's a bit more to it. The covariance is
> >> >> the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When
> >> >> there is no correlation, the deviations about the mean are random and
> >> >> average out to zero. But with the deviations against a reference, that
> >> >> is not the case. So the results should be regarded meaningless, unless
> >> >> you have a good reason for doing so, and come with a solid
> >> >&g

Re: [gmx-users] g_covar -ref

[Tsjerk Wassenaar]

Hi Vijaya,

> Your answer truly eludes me, unless -ref is an useless option.

Well, that's pretty close to the conclusion. The use is limited to a
few very specific cases and it might be better to hide the option from
the view of casual users.

But apparently you didn't catch the why yet. If you imagine a pendulum
going back and forth, the principal components will be commonly
determined by taking the deviations from the mean position. Then you
get two components, one for the direction of the motion and one for
the deflection from linearity, right? But now, you calculate  the
deviations not with respect to the average position, but you take the
deviations with respect to a position that is away from the mean, say
halfway to the left. Now you can follow the same procedure,
calculating a matrix of cross products for these deviations, and
diagonalizing it. But what do these 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-users] g_covar -ref
>> From: tsje...@gmail.com
>> To: gmx-users@gromacs.org
>>
>> Hi Vijaya,
>>
>> I'm sorry if I didn't quite get that first sentence of yours. Did you
>> meant to start it with "I thought that ..."? Or were you trying to
>> explain me something you thought I missed?
>>
>> PCA stands for 'principal component analysis', not 'covariance
>> analysis'. For instance, PCA can be applied to correlations, and then
>> is 'correlation analysis'. SVD is a particular flavour of PCA and here
>> yields the same results as traditional PCA because the covariance
>> matrix is symmetric, but otherwise they're not strictly the same. That
>> is to say, the SVD is obtained by extracting the eigenvectors from the
>> matrices transpose(S) x S and S x transpose(S). Which are quite
>> obviously identical if S is a symmetric matrix.
>>
>> By the way, was your question regarding the -ref option answered, or
>> did the answer elude you? If the latter is the case, maybe if now you
>> feel sufficiently confident that I know a bit about PCA, you can go
>> through the answer again.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Thu, Mar 18, 2010 at 7:01 PM, vijaya subramanian
>>  wrote:
>> > PCA refers to covariance analysis (though SVD gives the same results).
>> > Principal components are obtained 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 -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 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 still be finite, in stead of zero, as would
>> >> probably be most meaningful.
>> >> Now for the covariances, there's a bit more to it. The covariance is
>> >> the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When
>> >> there is no correlation, the deviations about the mean are random and
>> >> average out to zero. But with the deviations against a reference, that
>> >> is not the case. So the results should be regarded meaningless, unless
>> >> you have a good reason for doing so, and come with a solid
>> >> justification. Okay, there may be a purpose, but I'll leave that to
>> >> your imagination :)
>> >>
>> >> Hope it helps,
>> >>
>> >> Tsjerk
>> >>
>> >> On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian
>> >>  wrote:
>> >> > 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?
>> >&g

RE: [gmx-users] g_covar -ref

[vijaya subramanian]

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 get that first sentence of yours. Did you
> meant to start it with "I thought that ..."? Or were you trying to
> explain me something you thought I missed?
> 
> PCA stands for 'principal component analysis', not 'covariance
> analysis'. For instance, PCA can be applied to correlations, and then
> is 'correlation analysis'. SVD is a particular flavour of PCA and here
> yields the same results as traditional PCA because the covariance
> matrix is symmetric, but otherwise they're not strictly the same. That
> is to say, the SVD is obtained by extracting the eigenvectors from the
> matrices transpose(S) x S and S x transpose(S). Which are quite
> obviously identical if S is a symmetric matrix.
> 
> By the way, was your question regarding the -ref option answered, or
> did the answer elude you? If the latter is the case, maybe if now you
> feel sufficiently confident that I know a bit about PCA, you can go
> through the answer again.
> 
> Cheers,
> 
> Tsjerk
> 
> On Thu, Mar 18, 2010 at 7:01 PM, vijaya subramanian
>  wrote:
> > PCA refers to covariance analysis (though SVD gives the same results).
> > Principal components are obtained 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 -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 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 still be finite, in stead of zero, as would
> >> probably be most meaningful.
> >> Now for the covariances, there's a bit more to it. The covariance is
> >> the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When
> >> there is no correlation, the deviations about the mean are random and
> >> average out to zero. But with the deviations against a reference, that
> >> is not the case. So the results should be regarded meaningless, unless
> >> you have a good reason for doing so, and come with a solid
> >> justification. Okay, there may be a purpose, but I'll leave that to
> >> your imagination :)
> >>
> >> Hope it helps,
> >>
> >> Tsjerk
> >>
> >> On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian
> >>  wrote:
> >> > 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
> >> >
> >> >
> >> >
> >> > 
> >> > Hotmail: Trusted email with powerful SPAM protection. Sign up now.
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> >>
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Re: [gmx-users] g_covar -ref

[Tsjerk Wassenaar]

Hi Vijaya,

I'm sorry if I didn't quite get that first sentence of yours. Did you
meant to start it with "I thought that ..."? Or were you trying to
explain me something you thought I missed?

PCA stands for 'principal component analysis', not 'covariance
analysis'. For instance, PCA can be applied to correlations, and then
is 'correlation analysis'. SVD is a particular flavour of PCA and here
yields the same results as traditional PCA because the covariance
matrix is symmetric, but otherwise they're not strictly the same. That
is to say, the SVD is obtained by extracting the eigenvectors from the
matrices transpose(S) x S and S x transpose(S). Which are quite
obviously identical if S is a symmetric matrix.

By the way, was your question regarding the -ref option answered, or
did the answer elude you? If the latter is the case, maybe if now you
feel sufficiently confident that I know a bit about PCA, you can go
through the answer again.

Cheers,

Tsjerk

On Thu, Mar 18, 2010 at 7:01 PM, vijaya subramanian
 wrote:
> PCA refers to covariance analysis (though SVD gives the same results).
> Principal components are obtained 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 -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 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 still be finite, in stead of zero, as would
>> probably be most meaningful.
>> Now for the covariances, there's a bit more to it. The covariance is
>> the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When
>> there is no correlation, the deviations about the mean are random and
>> average out to zero. But with the deviations against a reference, that
>> is not the case. So the results should be regarded meaningless, unless
>> you have a good reason for doing so, and come with a solid
>> justification. Okay, there may be a purpose, but I'll leave that to
>> your imagination :)
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian
>>  wrote:
>> > 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
>> >
>> >
>> >
>> > 
>> > Hotmail: Trusted email with powerful SPAM protection. Sign up now.
>> > --
>> > gmx-users mailing list    gmx-us...@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at http://www.gromacs.org/search before
>> > posting!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.org.
>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> Groningen Institute for Biomolecular Research and Biotechnology
>> University of Groningen
>> The Netherlands
>> --
>> gmx-users mailing list gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
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>
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-- 
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post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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RE: [gmx-users] g_covar -ref

[vijaya subramanian]

PCA refers to covariance analysis (though SVD gives the same results).
Principal components are obtained 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 -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 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 still be finite, in stead of zero, as would
> probably be most meaningful.
> Now for the covariances, there's a bit more to it. The covariance is
> the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When
> there is no correlation, the deviations about the mean are random and
> average out to zero. But with the deviations against a reference, that
> is not the case. So the results should be regarded meaningless, unless
> you have a good reason for doing so, and come with a solid
> justification. Okay, there may be a purpose, but I'll leave that to
> your imagination :)
> 
> Hope it helps,
> 
> Tsjerk
> 
> On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian
>  wrote:
> > 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
> >
> >
> >
> > 
> > Hotmail: Trusted email with powerful SPAM protection. Sign up now.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> 
> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology
> University of Groningen
> The Netherlands
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] g_covar -ref

[Tsjerk Wassenaar]

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 still be finite, in stead of zero, as would
probably be most meaningful.
Now for the covariances, there's a bit more to it. The covariance is
the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When
there is no correlation, the deviations about the mean are random and
average out to zero. But with the deviations against a reference, that
is not the case. So the results should be regarded meaningless, unless
you have a good reason for doing so, and come with a solid
justification. Okay, there may be a purpose, but I'll leave that to
your imagination :)

Hope it helps,

Tsjerk

On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian
 wrote:
> 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
>
>
>
> 
> Hotmail: Trusted email with powerful SPAM protection. Sign up now.
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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Re: [gmx-users] g_covar ends up complaining from a Segmentation Fault

[Justin A. Lemkul]

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 need the .tpr file for mass-weighting, I believe.


Everything goes fine till the g_covar part where I get the
Segmentation fault! I don't have the slightest idea what this error
might want to convey!


Segmentation faults are general errors regarding memory allocation.  So no one 
here will have any idea what went wrong without seeing your command line, 
options chosen (if appropriate), etc.


-Justin


I have had the seg. fault error previously, where I found out that it
is caused by some miss-formatting in the files I edited manually. This
time I edited nothing myself though and all files were made by GMX
programs themselves!

Would be nice if I could get some comments, in case anyone has
encountered this before.

Thanks in advance,
greetings

Peyman


--
Peyman Yamin
Computational Structural Biology Group
Institut fuer Strukturbiologie und Biophysik (ISB)
ISB-3: Strukturbiochemie
Forschungszentrum Juelich
D-52425 Juelich
Tel:(49)-2461-61-4230
Fax:(49)-2461-61-2023


 

 


Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
 

 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] g_covar Segmentation fault

[Nicolas]

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 
you do that?
and made an index file of the entire system (45 beads). But now when I 
try to run g_covar using the group consisting the entire system, for 
least square fit and covariance analysis, it is giving Segmentation 
Fault. Am I doing anything wrong. Any suggestion is welcome.
You probably also need a tpr file. To create it, you need the parameters 
of your force field (in Gromacs format), the topology of each molecule 
you've got in your system (still in Gromacs format) and to run grompp.  
Depending on the original format of your force field, in can be quite 
difficult to do the file format conversion.


Hope that helps...
Nicolas


Regards,
 
 
*Anirban Ghosh*

*Grade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India
*



Add more friends to your messenger and enjoy! Invite them now. 
 




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begin:vcard
fn:Nicolas Sapay
n:Sapay;Nicolas
org:University of Calgary;Biological department
adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada
email;internet:nsa...@ucalgary.ca
title:Post-doctoral fellow
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Re: [gmx-users] g_covar Segmentation fault

[Mark Abraham]

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 to run g_covar 
using the group consisting the entire system, for least square fit and 
covariance analysis, it is giving Segmentation Fault. Am I doing 
anything wrong. Any suggestion is welcome.


Yes you're doing something wrong, but if you don't tell us at least your 
command line and your full output, how might we be expected to help? :-)


Mark
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Re: [gmx-users] g_covar

[tangxuan]

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?

Mark
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Through the option -xpma, i can get a covariance map for the atoms, 
but the value of covariance can not be seen.

In my opinion, in the header of xpm file, these
"A  c #FF " /* "-0.011" */,
"B  c #1414FF " /* "-0.0102" */,
"C  c #2727FF " /* "-0.00935" */,
"D  c #3B3BFF " /* "-0.0085" */,
"E  c #4E4EFF " /* "-0.00765" */,
"F  c #6262FF " /* "-0.0068" */,
"G  c #7676FF " /* "-0.00595" */,
"H  c #8989FF " /* "-0.0051" */,
"I  c #9D9DFF " /* "-0.00425" */,
"J  c #B1B1FF " /* "-0.0034" */,
"K  c #C4C4FF " /* "-0.00255" */,
"L  c #D8D8FF " /* "-0.0017" */,
"M  c #EBEBFF " /* "-0.00085" */,
"N  c #FF " /* "0" */"
just give a range which the covariance value of atoms belong to.  
However, I want to get a value, but not a range for the covariance  
of atoms.


Yes, but that's not what I asked. What is unsatisfactory with the 
-ascii output?


Mark
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It is ok. I just want to know if i can convert the data in -ascii output 
to value of atom covariance.


Tang
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Re: [gmx-users] g_covar

[Mark Abraham]

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
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Through the option -xpma, i can get a covariance map for the atoms, but 
the value of covariance can not be seen.

In my opinion, in the header of xpm file, these
"A  c #FF " /* "-0.011" */,
"B  c #1414FF " /* "-0.0102" */,
"C  c #2727FF " /* "-0.00935" */,
"D  c #3B3BFF " /* "-0.0085" */,
"E  c #4E4EFF " /* "-0.00765" */,
"F  c #6262FF " /* "-0.0068" */,
"G  c #7676FF " /* "-0.00595" */,
"H  c #8989FF " /* "-0.0051" */,
"I  c #9D9DFF " /* "-0.00425" */,
"J  c #B1B1FF " /* "-0.0034" */,
"K  c #C4C4FF " /* "-0.00255" */,
"L  c #D8D8FF " /* "-0.0017" */,
"M  c #EBEBFF " /* "-0.00085" */,
"N  c #FF " /* "0" */"
just give a range which the covariance value of atoms belong to.  
However, I want to get a value, but not a range for the covariance  of 
atoms.


Yes, but that's not what I asked. What is unsatisfactory with the -ascii 
output?


Mark
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Re: [gmx-users] g_covar

[tangxuan]

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
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Through the option -xpma, i can get a covariance map for the atoms, but 
the value of covariance can not be seen.

In my opinion, in the header of xpm file, these
"A  c #FF " /* "-0.011" */,
"B  c #1414FF " /* "-0.0102" */,
"C  c #2727FF " /* "-0.00935" */,
"D  c #3B3BFF " /* "-0.0085" */,
"E  c #4E4EFF " /* "-0.00765" */,
"F  c #6262FF " /* "-0.0068" */,
"G  c #7676FF " /* "-0.00595" */,
"H  c #8989FF " /* "-0.0051" */,
"I  c #9D9DFF " /* "-0.00425" */,
"J  c #B1B1FF " /* "-0.0034" */,
"K  c #C4C4FF " /* "-0.00255" */,
"L  c #D8D8FF " /* "-0.0017" */,
"M  c #EBEBFF " /* "-0.00085" */,
"N  c #FF " /* "0" */"
just give a range which the covariance value of atoms belong to.  
However, I want to get a value, but not a range for the covariance  of 
atoms.


Tang


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Re: [gmx-users] g_covar

[Mark Abraham]

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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Re: [gmx-users] g_covar

[tangxuan]

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 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 
command, I used trr file and tpr file of the whole system. Do I have to 
get a new trr file and tpr file just for these alpha carbons? 
Some information  is shown below.

"Group 0 (  System) has 293401 elements
Group 1 ( Protein) has 75295 elements
Group 2 (   Protein-H) has 38096 elements
Group 3 ( C-alpha) has  4831 elements
Group 4 (Backbone) has 14493 elements
Group 5 (   MainChain) has 19340 elements
Group 6 (MainChain+Cb) has 23750 elements
Group 7 ( MainChain+H) has 23963 elements
Group 8 (   SideChain) has 51332 elements
Group 9 ( SideChain-H) has 18756 elements
Group10 ( Prot-Masses) has 75295 elements
Group11 ( Non-Protein) has 218106 elements
Group12 ( KCX) has   184 elements
.
.
Group   107 (chO_chV_&_C-alpha) has   929 elements
Select a group: 107
Selected 107: 'chO_chV_&_C-alpha'
Calculating the average structure ...
trn version: GMX_trn_file (single precision)
Reading frame   0 time 2.000  
WARNING number of atoms in tpx (929) and trajectory (293401) do not match
Last frame   1000 time 3.000  


Last frame   1000 time 3.000   to ./#average.pdb.17#
Read 1001 frames

Trace of the covariance matrix: 2.34563 (nm^2)
100%
Diagonalizing ...

Sum of the eigenvalues: 2.34563 (nm^2)

Writing eigenvalues to eigenval.xvg

Writing reference, average structure & eigenvectors 1--1000 to eigenvec.trr
Wrote the log to covar.log"

Tang


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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?


Thanks

Tang
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RE: [gmx-users] g_covar

[Berk Hess]

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 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 
> command, I used trr file and tpr file of the whole system. Do I have to 
> get a new trr file and tpr file just for these alpha carbons? 
> Some information  is shown below.
> "Group 0 (  System) has 293401 elements
> Group 1 ( Protein) has 75295 elements
> Group 2 (   Protein-H) has 38096 elements
> Group 3 ( C-alpha) has  4831 elements
> Group 4 (Backbone) has 14493 elements
> Group 5 (   MainChain) has 19340 elements
> Group 6 (MainChain+Cb) has 23750 elements
> Group 7 ( MainChain+H) has 23963 elements
> Group 8 (   SideChain) has 51332 elements
> Group 9 ( SideChain-H) has 18756 elements
> Group10 ( Prot-Masses) has 75295 elements
> Group11 ( Non-Protein) has 218106 elements
> Group12 ( KCX) has   184 elements
> .
> .
> Group   107 (chO_chV_&_C-alpha) has   929 elements
> Select a group: 107
> Selected 107: 'chO_chV_&_C-alpha'
> Calculating the average structure ...
> trn version: GMX_trn_file (single precision)
> Reading frame   0 time 2.000  
> WARNING number of atoms in tpx (929) and trajectory (293401) do not match
> Last frame   1000 time 3.000  
> 
> Last frame   1000 time 3.000   to ./#average.pdb.17#
> Read 1001 frames
> 
> Trace of the covariance matrix: 2.34563 (nm^2)
> 100%
> Diagonalizing ...
> 
> Sum of the eigenvalues: 2.34563 (nm^2)
> 
> Writing eigenvalues to eigenval.xvg
> 
> Writing reference, average structure & eigenvectors 1--1000 to eigenvec.trr
> Wrote the log to covar.log"
> 
> Tang
> 
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to [EMAIL PROTECTED]
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