[gmx-users] Dynamic cross correlation map

[sukesh chandra gain]

Dear All,

Could you please tell how to plot the Dynamic Cross Correlation Matrix 
with Gromacs analysis tool or other tools. I want to know over a 20 ns 
simulation whether the motions of two residues or group of residues are 
correlated or anti correlated. For this I want to plot a dynamics cross 
correlation map in which I could get the precise information of group of 
atoms.
I have done the following step and got the covariance matrix but don't 
know how to proceed further.
>g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l 
covar.log -xpm covar.xpm -ascii covar.dat

Waiting for your input.

Thank You,
Regards,
Sukesh

--
Sukesh Chandra Gain
TCS Innovation Labs
Tata Consultancy Services Ltd.
'Deccan Park', Madhapur
Hyderabad 500081
Phone:  +91 40 6667 3572

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RE: [gmx-users] dynamic cross correlation map (DCCM)

[Berk Hess]

Hi,

g_covar -xpm or -ascii gives you the complete covariance matrix.
This contains all the correlations.
I could be that DCCM gives the matrix normalized with the square root
of the product of the diagonal, which is the normalized correlation.
This would be a useful option which I might put into g_covar.
But you can do this yourself with a small script on the -ascii output.

Berk

> Date: Tue, 19 Jan 2010 13:23:30 +0100
> Subject: Re: [gmx-users] dynamic cross correlation map (DCCM)
> From: tsje...@gmail.com
> To: jalem...@vt.edu; gmx-users@gromacs.org
> CC: 
> 
> Hi,
> 
> Well I'd say that 'DCCM' refers to the matrix (map) of correlations
> and not to that of covariances. More specifically, it refers to
> correlations of positional fluctuations. PCA, on the other hand,
> refers to the extraction of components or axes which better describe
> the data than the original axes do, not specifying what kind of data,
> nor whether correlations or covariances be used for their
> determination. That's quite a distinction.
> g_covar gives the covariance matrix, not the correlation matrix. I
> believe there was a modified version in the contributions section
> which was able to compute correlations.
> 
> Cheers,
> 
> Tsjerk
> 
> 
> On Tue, Jan 19, 2010 at 12:50 PM, Justin A. Lemkul  wrote:
> >
> >
> > leila karami wrote:
> >>
> >> Hi
> >>  I want to obtain dynamic cross correlation map (DCCM). I used following
> >> command for obtaining covariance matrix.
> >>  g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l
> >> covar.log -xpm covar.xpm.
> >>  my system consists protein of 70 aminoacids. I want survey correlated and
> >> anti-correlated motion between residues.
> >>  Is my manner true? If so, which of output files in above give me dynamic
> >> cross correlation map (DCCM)? otherwise, please guide me.
> >>
> >
> > No one has ever been able to explain to me the difference between DCCM and
> > PCA, so I'd say you're correct at least in obtaining the covariance matrix,
> > which will give you information about correlated and anticorrelated motion.
> >  "DCCM" seems to be a popular term with the AMBER crowd, but I don't know
> > that their manual even gives the equations used for such an analysis to
> > potentially differentiate it from PCA.  I believe there are some tips in
> > their mail reflector, however.
> >
> > -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
> >
> > 
> > --
> > 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.
> 
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] dynamic cross correlation map (DCCM)

[Tsjerk Wassenaar]

Hi,

Well I'd say that 'DCCM' refers to the matrix (map) of correlations
and not to that of covariances. More specifically, it refers to
correlations of positional fluctuations. PCA, on the other hand,
refers to the extraction of components or axes which better describe
the data than the original axes do, not specifying what kind of data,
nor whether correlations or covariances be used for their
determination. That's quite a distinction.
g_covar gives the covariance matrix, not the correlation matrix. I
believe there was a modified version in the contributions section
which was able to compute correlations.

Cheers,

Tsjerk


On Tue, Jan 19, 2010 at 12:50 PM, Justin A. Lemkul  wrote:
>
>
> leila karami wrote:
>>
>> Hi
>>  I want to obtain dynamic cross correlation map (DCCM). I used following
>> command for obtaining covariance matrix.
>>  g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l
>> covar.log -xpm covar.xpm.
>>  my system consists protein of 70 aminoacids. I want survey correlated and
>> anti-correlated motion between residues.
>>  Is my manner true? If so, which of output files in above give me dynamic
>> cross correlation map (DCCM)? otherwise, please guide me.
>>
>
> No one has ever been able to explain to me the difference between DCCM and
> PCA, so I'd say you're correct at least in obtaining the covariance matrix,
> which will give you information about correlated and anticorrelated motion.
>  "DCCM" seems to be a popular term with the AMBER crowd, but I don't know
> that their manual even gives the equations used for such an analysis to
> potentially differentiate it from PCA.  I believe there are some tips in
> their mail reflector, however.
>
> -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
>
> 
> --
> 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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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] dynamic cross correlation map (DCCM)

[Justin A. Lemkul]

leila karami wrote:

Hi
 
I want to obtain dynamic cross correlation map (DCCM). I used following 
command for obtaining covariance matrix.
 
g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l 
covar.log -xpm covar.xpm.
 
my system consists protein of 70 aminoacids. I want survey correlated 
and anti-correlated motion between residues.
 
Is my manner true? If so, which of output files in above give me dynamic 
cross correlation map (DCCM)? otherwise, please guide me.




No one has ever been able to explain to me the difference between DCCM and PCA, 
so I'd say you're correct at least in obtaining the covariance matrix, which 
will give you information about correlated and anticorrelated motion.  "DCCM" 
seems to be a popular term with the AMBER crowd, but I don't know that their 
manual even gives the equations used for such an analysis to potentially 
differentiate it from PCA.  I believe there are some tips in their mail 
reflector, however.


-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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[gmx-users] dynamic cross correlation map (DCCM)

[leila karami]

Hi

I want to obtain dynamic cross correlation map (DCCM). I used following
command for obtaining covariance matrix.

g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l
covar.log -xpm covar.xpm.

my system consists protein of 70 aminoacids. I want survey correlated and
anti-correlated motion between residues.

Is my manner true? If so, which of output files in above give me dynamic
cross correlation map (DCCM)? otherwise, please guide me.
-- 
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[gmx-users] dynamic cross correlation map (DCCM)

[leila karami]

Hi

I want to obtain dynamic cross correlation map (DCCM). I used following
command for obtaining covariance matrix.

g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l
covar.log -xpm covar.xpm.

my system consists protein of 70 aminoacids. I want survey correlated and
anti-correlated motion between residues.

Is my manner true? If so, which of output files in above give me dynamic
cross correlation map (DCCM)? otherwise, please guide me.
-- 
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Re: [gmx-users] dynamic cross correlation map

[Qi Yan]

Hi, all:

Does anybody know how to normalize the covariance matrix generated by
g_covar with option -xpma. For -ascii, these data is the whole
covariance matrix, which means the number in the matrix is 3N*3N (N is
the number of atoms and I just choose alpha C). Now, I want to get the
atomic covariance matrix for each atom pair the sum of the xx, yy and
zz. I know -xpma can implement that, but the results is not normalized,
it is hard to compared each other. So, I hope someone can tell me what
should I do now?

Thanks in advance.

Qi Yan

I think g_covar -ascii is what you are looking for.
I have a Maple script that does this kind of graph. If you want you can
contact me off list.

Regards.

Pedro.

2007/9/18, Dhananjay <[EMAIL PROTECTED]>:
>
> Well, I have done 30ns MD simulation for a protein. The protein
consists
> of 4 loop regions.
> Using g_cover programme the covariance matrix have been generated and
> using g_anaeig programme with option -rmsf , along first 8 eigen
vectors the
> rms fluction of c-alpha atoms were plotted.
> But this is giving me just the information that  particular atom is
> fluctuating along particular direction.
> I want to know over a 30 ns simulation whether the motions of two
atoms or
> group of two atoms are correlated or anti correlated. For this I want
to
> form a dynamics cross correlation map in which I could get the precise
> information of group of atoms. The function  used for this kind of
analysis
> is
>
> C(i,j) = < delta r(i) * delta r(j) > /  sqrt < sqr(delta r(i) ) > .
sqrt <
> sqr(delta r(j) ) >
>
> the positive C(i,j) -> motions are correlated
> the negative C(i,j) -> motions are anti-correlated
>
> I want to plot a 2-D map indicated correlated and anti-correlated
motions.
>
>
> My question is whether it is possible in GROMACS to plot this king of
map
> or could you please suggest any other free software which could read
the
> trajectories generated by GROMACS and plot the map.
>
> Again thanking you in advance ..
>
>
> -- Dhananjay
>
>
>
>
> On 9/18/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
> >
> > Dhananjay wrote:for each atom pair the sum of the xx, yy and zz
covariances
> > > This may be bit different question from main theme.
> > >
> > > I want to form dynamic cross correlation map as I have
trajectories
> > > generated by GROMACS 3.3.
> > >
> > > Please suggest me free software which can read the .trr file for
> > > plotting DCCM (dynamic cross correlation map )
> > try g_covar or otherwise explain in more detail (equations) what you
> > want to do.
> >
> > >
> > > Thanking you in advance
> > >
> > >
> > >
> > > --  Dhananjay
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Re: [gmx-users] dynamic cross correlation map

[David van der Spoel]

Dhananjay wrote:

Thanks you Tsjerk and all,

Yes, the request was for residue correlations. Sorry for not mentioning 
it precisely.

I will workout the solutions that were suggested here.

But still, how can I get residue–residue-based correlated motions map ? 


It's matter of how you define it. An easy way would be to try C-alphas.



Any other way or software ?



-- Dhananjay


On 9/18/07, *Yang Ye* <[EMAIL PROTECTED]  
 > wrote:


g_traj to extract  coordinates, velocities, forces into xvg files for
you perform calculation.

On 9/18/2007 8:20 PM, Dhananjay wrote:
 > Well, I have done 30ns MD simulation for a protein. The protein
 > consists of 4 loop regions.
 > Using g_cover programme the covariance matrix have been generated
and
 > using g_anaeig programme with option -rmsf , along first 8 eigen
 > vectors the rms fluction of c-alpha atoms were plotted.
 > But this is giving me just the information that  particular atom is
 > fluctuating along particular direction.
 > I want to know over a 30 ns simulation whether the motions of two
 > atoms or group of two atoms are correlated or anti correlated. For
 > this I want to form a dynamics cross correlation map in which I
could
 > get the precise information of group of atoms. The function  used for
 > this kind of analysis is
 >
 > C(i,j) = < delta r(i) * delta r(j) > /  sqrt < sqr(delta r(i) ) > .
 > sqrt < sqr(delta r(j) ) >
 >
 > the positive C(i,j) -> motions are correlated
 > the negative C(i,j) -> motions are anti-correlated
 >
 > I want to plot a 2-D map indicated correlated and anti-correlated
 > motions.
 >
 > My question is whether it is possible in GROMACS to plot this king of
 > map or could you please suggest any other free software which could
 > read the trajectories generated by GROMACS and plot the map.
 >
 > Again thanking you in advance ..
 >
 >
 > -- Dhananjay
 >
 >
 >
 >
 > On 9/18/07, *David van der Spoel* <[EMAIL PROTECTED]

 > >> wrote:
 >
 > Dhananjay wrote:
 > > This may be bit different question from main theme.
 > >
 > > I want to form dynamic cross correlation map as I have
trajectories
 > > generated by GROMACS 3.3.
 > >
 > > Please suggest me free software which can read the .trr
file for
 > > plotting DCCM (dynamic cross correlation map )
 > try g_covar or otherwise explain in more detail (equations)
what you
 > want to do.
 >
 > >
 > > Thanking you in advance
 > >
 > >
 > >
 > > --  Dhananjay
 > >
 > >
 > >
 >


 > >
 > > ___
 > > gmx-users mailing listgmx-users@gromacs.org

 > mailto:gmx-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]

 > >.
 > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 >
 >
 > --
 > David van der Spoel, Ph.D.
 > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
 > University.
 > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax:
 > +4618511755.
 > [EMAIL PROTECTED] 
 > mailto:[EMAIL PROTECTED]>>[EMAIL PROTECTED]

 > >  
http://folding.bmc.uu.se 

 > ___
 > gmx-users mailing list gmx-users@gromacs.org

 > mailto:gmx-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]

 > >.
 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 >
 >
 >
 >
 > --
 > Dhananjay C Joshi
 > Project Assistant
 > LT & LSB, C D F D
 > ECIL Road, Nacharam
 > Hy

Re: [gmx-users] dynamic cross correlation map

[Dhananjay]

Thanks you Tsjerk and all,

Yes, the request was for residue correlations. Sorry for not mentioning it
precisely.
I will workout the solutions that were suggested here.

But still, how can I get residue–residue-based correlated motions map ?

Any other way or software ?



-- Dhananjay


On 9/18/07, Yang Ye <[EMAIL PROTECTED]> wrote:
>
> g_traj to extract  coordinates, velocities, forces into xvg files for
> you perform calculation.
>
> On 9/18/2007 8:20 PM, Dhananjay wrote:
> > Well, I have done 30ns MD simulation for a protein. The protein
> > consists of 4 loop regions.
> > Using g_cover programme the covariance matrix have been generated and
> > using g_anaeig programme with option -rmsf , along first 8 eigen
> > vectors the rms fluction of c-alpha atoms were plotted.
> > But this is giving me just the information that  particular atom is
> > fluctuating along particular direction.
> > I want to know over a 30 ns simulation whether the motions of two
> > atoms or group of two atoms are correlated or anti correlated. For
> > this I want to form a dynamics cross correlation map in which I could
> > get the precise information of group of atoms. The function  used for
> > this kind of analysis is
> >
> > C(i,j) = < delta r(i) * delta r(j) > /  sqrt < sqr(delta r(i) ) > .
> > sqrt < sqr(delta r(j) ) >
> >
> > the positive C(i,j) -> motions are correlated
> > the negative C(i,j) -> motions are anti-correlated
> >
> > I want to plot a 2-D map indicated correlated and anti-correlated
> > motions.
> >
> > My question is whether it is possible in GROMACS to plot this king of
> > map or could you please suggest any other free software which could
> > read the trajectories generated by GROMACS and plot the map.
> >
> > Again thanking you in advance ..
> >
> >
> > -- Dhananjay
> >
> >
> >
> >
> > On 9/18/07, *David van der Spoel* <[EMAIL PROTECTED]
> > > wrote:
> >
> > Dhananjay wrote:
> > > This may be bit different question from main theme.
> > >
> > > I want to form dynamic cross correlation map as I have
> trajectories
> > > generated by GROMACS 3.3.
> > >
> > > Please suggest me free software which can read the .trr file for
> > > plotting DCCM (dynamic cross correlation map )
> > try g_covar or otherwise explain in more detail (equations) what you
> > want to do.
> >
> > >
> > > Thanking you in advance
> > >
> > >
> > >
> > > --  Dhananjay
> > >
> > >
> > >
> >
> 
> > >
> > > ___
> > > 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]
> > .
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > --
> > David van der Spoel, Ph.D.
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
> > University.
> > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax:
> > +4618511755.
> > [EMAIL PROTECTED]
> > [EMAIL PROTECTED]
> >    http://folding.bmc.uu.se
> > ___
> > gmx-users mailing list gmx-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]
> > .
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> >
> >
> > --
> > Dhananjay C Joshi
> > Project Assistant
> > LT & LSB, C D F D
> > ECIL Road, Nacharam
> > Hyderabad-500 076, INDIA
> > Tel : +91-40-27151344
> > Fax : +91-40-27155610
> > 
> >
> > ___
> > 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!
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>
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Re: [gmx-users] dynamic cross correlation map

[Yang Ye]

g_traj to extract  coordinates, velocities, forces into xvg files for 
you perform calculation.


On 9/18/2007 8:20 PM, Dhananjay wrote:
Well, I have done 30ns MD simulation for a protein. The protein 
consists of 4 loop regions.
Using g_cover programme the covariance matrix have been generated and 
using g_anaeig programme with option -rmsf , along first 8 eigen 
vectors the rms fluction of c-alpha atoms were plotted.
But this is giving me just the information that  particular atom is 
fluctuating along particular direction.
I want to know over a 30 ns simulation whether the motions of two 
atoms or group of two atoms are correlated or anti correlated. For 
this I want to form a dynamics cross correlation map in which I could 
get the precise information of group of atoms. The function  used for 
this kind of analysis is


C(i,j) = < delta r(i) * delta r(j) > /  sqrt < sqr(delta r(i) ) > . 
sqrt < sqr(delta r(j) ) >


the positive C(i,j) -> motions are correlated
the negative C(i,j) -> motions are anti-correlated

I want to plot a 2-D map indicated correlated and anti-correlated 
motions.


My question is whether it is possible in GROMACS to plot this king of 
map or could you please suggest any other free software which could 
read the trajectories generated by GROMACS and plot the map.


Again thanking you in advance ..


-- Dhananjay




On 9/18/07, *David van der Spoel* <[EMAIL PROTECTED] 
> wrote:


Dhananjay wrote:
> This may be bit different question from main theme.
>
> I want to form dynamic cross correlation map as I have trajectories
> generated by GROMACS 3.3.
>
> Please suggest me free software which can read the .trr file for
> plotting DCCM (dynamic cross correlation map )
try g_covar or otherwise explain in more detail (equations) what you
want to do.

>
> Thanking you in advance
>
>
>
> --  Dhananjay
>
>
>

>
> ___
> 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!
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.
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax:
+4618511755.
[EMAIL PROTECTED]
[EMAIL PROTECTED]
   http://folding.bmc.uu.se
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Dhananjay C Joshi
Project Assistant
LT & LSB, C D F D
ECIL Road, Nacharam
Hyderabad-500 076, INDIA
Tel : +91-40-27151344
Fax : +91-40-27155610


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Re: [gmx-users] dynamic cross correlation map

[Tsjerk Wassenaar]

Hi,

g_covar -h says that -xpma gives the cross-covariance, not the correlation...
Also, I believe the request was for residue correlations, although not
specified in what way. Anyway, at present g_covar does not give
correlations, but that is easy enough. g_covar -ascii gives a raw
covariance matrix, of which the sqrt of the diagonal elements can be
used to obtain the correlations, but that won't yet give the residue
correlations.

Tsjerk

On 9/18/07, Berk Hess <[EMAIL PROTECTED]> wrote:
> What do you need the Maple script for?
> Averaging over atoms in groups?
>
> g_covar -xpma gives exactly the cross correlation for each atom pair.
>
> Berk.
>
> >
> >I think g_covar -ascii is what you are looking for.
> >I have a Maple script that does this kind of graph. If you want you can
> >contact me off list.
> >
> >Regards.
> >
> >Pedro.
> >
> >2007/9/18, Dhananjay <[EMAIL PROTECTED]>:
> > >
> > > Well, I have done 30ns MD simulation for a protein. The protein consists
> > > of 4 loop regions.
> > > Using g_cover programme the covariance matrix have been generated and
> > > using g_anaeig programme with option -rmsf , along first 8 eigen vectors
> >the
> > > rms fluction of c-alpha atoms were plotted.
> > > But this is giving me just the information that  particular atom is
> > > fluctuating along particular direction.
> > > I want to know over a 30 ns simulation whether the motions of two atoms
> >or
> > > group of two atoms are correlated or anti correlated. For this I want to
> > > form a dynamics cross correlation map in which I could get the precise
> > > information of group of atoms. The function  used for this kind of
> >analysis
> > > is
> > >
> > > C(i,j) = < delta r(i) * delta r(j) > /  sqrt < sqr(delta r(i) ) > . sqrt
> ><
> > > sqr(delta r(j) ) >
> > >
> > > the positive C(i,j) -> motions are correlated
> > > the negative C(i,j) -> motions are anti-correlated
> > >
> > > I want to plot a 2-D map indicated correlated and anti-correlated
> >motions.
> > >
> > >
> > > My question is whether it is possible in GROMACS to plot this king of
> >map
> > > or could you please suggest any other free software which could read the
> > > trajectories generated by GROMACS and plot the map.
> > >
> > > Again thanking you in advance ..
> > >
> > >
> > > -- Dhananjay
> > >
> > >
> > >
> > >
> > > On 9/18/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
> > > >
> > > > Dhananjay wrote:
> > > > > This may be bit different question from main theme.
> > > > >
> > > > > I want to form dynamic cross correlation map as I have trajectories
> > > > > generated by GROMACS 3.3.
> > > > >
> > > > > Please suggest me free software which can read the .trr file for
> > > > > plotting DCCM (dynamic cross correlation map )
> > > > try g_covar or otherwise explain in more detail (equations) what you
> > > > want to do.
> > > >
> > > > >
> > > > > Thanking you in advance
> > > > >
> > > > >
> > > > >
> > > > > --  Dhananjay
> > > > >
> > > > >
> > > > >
> > > >
> >
> > > > >
> > > > > ___
> > > > > 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]
> > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > >
> > > >
> > > > --
> > > > David van der Spoel, Ph.D.
> > > > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
> >University.
> > > > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax:
> >+4618511755.
> > > > [EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
> > > > ___
> > > > gmx-users mailing list gmx-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] .
> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > >
> > >
> > >
> > >
> > > --
> > > Dhananjay C Joshi
> > > Project Assistant
> > > LT & LSB, C D F D
> > > ECIL Road, Nacharam
> > > Hyderabad-500 076, INDIA
> > > Tel : +91-40-27151344
> > > Fax : +91-40-27155610
> > > ___
> > > 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]
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
>
>
> >_

Re: [gmx-users] dynamic cross correlation map

[Berk Hess]

What do you need the Maple script for?
Averaging over atoms in groups?

g_covar -xpma gives exactly the cross correlation for each atom pair.

Berk.



I think g_covar -ascii is what you are looking for.
I have a Maple script that does this kind of graph. If you want you can
contact me off list.

Regards.

Pedro.

2007/9/18, Dhananjay <[EMAIL PROTECTED]>:
>
> Well, I have done 30ns MD simulation for a protein. The protein consists
> of 4 loop regions.
> Using g_cover programme the covariance matrix have been generated and
> using g_anaeig programme with option -rmsf , along first 8 eigen vectors 
the

> rms fluction of c-alpha atoms were plotted.
> But this is giving me just the information that  particular atom is
> fluctuating along particular direction.
> I want to know over a 30 ns simulation whether the motions of two atoms 
or

> group of two atoms are correlated or anti correlated. For this I want to
> form a dynamics cross correlation map in which I could get the precise
> information of group of atoms. The function  used for this kind of 
analysis

> is
>
> C(i,j) = < delta r(i) * delta r(j) > /  sqrt < sqr(delta r(i) ) > . sqrt 
<

> sqr(delta r(j) ) >
>
> the positive C(i,j) -> motions are correlated
> the negative C(i,j) -> motions are anti-correlated
>
> I want to plot a 2-D map indicated correlated and anti-correlated 
motions.

>
>
> My question is whether it is possible in GROMACS to plot this king of 
map

> or could you please suggest any other free software which could read the
> trajectories generated by GROMACS and plot the map.
>
> Again thanking you in advance ..
>
>
> -- Dhananjay
>
>
>
>
> On 9/18/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
> >
> > Dhananjay wrote:
> > > This may be bit different question from main theme.
> > >
> > > I want to form dynamic cross correlation map as I have trajectories
> > > generated by GROMACS 3.3.
> > >
> > > Please suggest me free software which can read the .trr file for
> > > plotting DCCM (dynamic cross correlation map )
> > try g_covar or otherwise explain in more detail (equations) what you
> > want to do.
> >
> > >
> > > Thanking you in advance
> > >
> > >
> > >
> > > --  Dhananjay
> > >
> > >
> > >
> > 


> > >
> > > ___
> > > 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]
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > --
> > David van der Spoel, Ph.D.
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala 
University.
> > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: 
+4618511755.

> > [EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
> > ___
> > gmx-users mailing list gmx-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] .
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Dhananjay C Joshi
> Project Assistant
> LT & LSB, C D F D
> ECIL Road, Nacharam
> Hyderabad-500 076, INDIA
> Tel : +91-40-27151344
> Fax : +91-40-27155610
> ___
> 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]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>




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Re: [gmx-users] dynamic cross correlation map

[Pedro Alexandre de Araújo Gomes Lapido Loureiro]

I think g_covar -ascii is what you are looking for.
I have a Maple script that does this kind of graph. If you want you can
contact me off list.

Regards.

Pedro.

2007/9/18, Dhananjay <[EMAIL PROTECTED]>:
>
> Well, I have done 30ns MD simulation for a protein. The protein consists
> of 4 loop regions.
> Using g_cover programme the covariance matrix have been generated and
> using g_anaeig programme with option -rmsf , along first 8 eigen vectors the
> rms fluction of c-alpha atoms were plotted.
> But this is giving me just the information that  particular atom is
> fluctuating along particular direction.
> I want to know over a 30 ns simulation whether the motions of two atoms or
> group of two atoms are correlated or anti correlated. For this I want to
> form a dynamics cross correlation map in which I could get the precise
> information of group of atoms. The function  used for this kind of analysis
> is
>
> C(i,j) = < delta r(i) * delta r(j) > /  sqrt < sqr(delta r(i) ) > . sqrt <
> sqr(delta r(j) ) >
>
> the positive C(i,j) -> motions are correlated
> the negative C(i,j) -> motions are anti-correlated
>
> I want to plot a 2-D map indicated correlated and anti-correlated motions.
>
>
> My question is whether it is possible in GROMACS to plot this king of map
> or could you please suggest any other free software which could read the
> trajectories generated by GROMACS and plot the map.
>
> Again thanking you in advance ..
>
>
> -- Dhananjay
>
>
>
>
> On 9/18/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
> >
> > Dhananjay wrote:
> > > This may be bit different question from main theme.
> > >
> > > I want to form dynamic cross correlation map as I have trajectories
> > > generated by GROMACS 3.3.
> > >
> > > Please suggest me free software which can read the .trr file for
> > > plotting DCCM (dynamic cross correlation map )
> > try g_covar or otherwise explain in more detail (equations) what you
> > want to do.
> >
> > >
> > > Thanking you in advance
> > >
> > >
> > >
> > > --  Dhananjay
> > >
> > >
> > >
> > 
> > >
> > > ___
> > > 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]
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > --
> > David van der Spoel, Ph.D.
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> > [EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
> > ___
> > gmx-users mailing list gmx-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] .
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Dhananjay C Joshi
> Project Assistant
> LT & LSB, C D F D
> ECIL Road, Nacharam
> Hyderabad-500 076, INDIA
> Tel : +91-40-27151344
> Fax : +91-40-27155610
> ___
> 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
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>
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Re: [gmx-users] dynamic cross correlation map

[Dhananjay]

Well, I have done 30ns MD simulation for a protein. The protein consists of
4 loop regions.
Using g_cover programme the covariance matrix have been generated and using
g_anaeig programme with option -rmsf , along first 8 eigen vectors the rms
fluction of c-alpha atoms were plotted.
But this is giving me just the information that  particular atom is
fluctuating along particular direction.
I want to know over a 30 ns simulation whether the motions of two atoms or
group of two atoms are correlated or anti correlated. For this I want to
form a dynamics cross correlation map in which I could get the precise
information of group of atoms. The function  used for this kind of analysis
is

C(i,j) = < delta r(i) * delta r(j) > /  sqrt < sqr(delta r(i) ) > . sqrt <
sqr(delta r(j) ) >

the positive C(i,j) -> motions are correlated
the negative C(i,j) -> motions are anti-correlated

I want to plot a 2-D map indicated correlated and anti-correlated motions.

My question is whether it is possible in GROMACS to plot this king of map or
could you please suggest any other free software which could read the
trajectories generated by GROMACS and plot the map.

Again thanking you in advance ..


-- Dhananjay




On 9/18/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
>
> Dhananjay wrote:
> > This may be bit different question from main theme.
> >
> > I want to form dynamic cross correlation map as I have trajectories
> > generated by GROMACS 3.3.
> >
> > Please suggest me free software which can read the .trr file for
> > plotting DCCM (dynamic cross correlation map )
> try g_covar or otherwise explain in more detail (equations) what you
> want to do.
>
> >
> > Thanking you in advance
> >
> >
> >
> > --  Dhananjay
> >
> >
> > 
> >
> > ___
> > 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]
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> [EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
> ___
> 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]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Dhananjay C Joshi
Project Assistant
LT & LSB, C D F D
ECIL Road, Nacharam
Hyderabad-500 076, INDIA
Tel : +91-40-27151344
Fax : +91-40-27155610
___
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Re: [gmx-users] dynamic cross correlation map

[David van der Spoel]

Dhananjay wrote:

This may be bit different question from main theme.

I want to form dynamic cross correlation map as I have trajectories 
generated by GROMACS 3.3.


Please suggest me free software which can read the .trr file for 
plotting DCCM (dynamic cross correlation map )
try g_covar or otherwise explain in more detail (equations) what you 
want to do.




Thanking you in advance



--  Dhananjay




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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] dynamic cross correlation map

[Dhananjay]

This may be bit different question from main theme.

I want to form dynamic cross correlation map as I have trajectories
generated by GROMACS 3.3.

Please suggest me free software which can read the .trr file for plotting
DCCM (dynamic cross correlation map )

Thanking you in advance



--  Dhananjay
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