[gmx-users] Dynamics cross correlation map

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Mar 23 11:54:52 CET 2010

Hi Sukesh,

You've posted this question several times now, without changing the
phrasing. Did it occur to you that maybe nobody felt equipped to or
sufficiently triggered by your post to reply? What do you mean with a
'dynamics cross correlation map' for 'residues or groups of residues'?
Being more explicit, also pointing to some references or giving some
formulas, might help you get a response.
But isn't your answer already in the image covar.xpm? Otherwise, maybe
using the atomic covariances (-xpma) might do what you want. If not,
your problem is not as trivial as you may think.



On Tue, Mar 23, 2010 at 11:44 AM, sukesh chandra gain
<sukesh at atc.tcs.com> wrote:
> Dear All,
> Could you please tell how to get the Dynamic Cross Correlation map 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
> --
> gmx-users mailing list    gmx-users at 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-request at 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

More information about the gromacs.org_gmx-users mailing list