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

2010-01-19 Thread Berk Hess
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: > >

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

2010-01-19 Thread 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 a

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

2010-01-19 Thread 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 surve

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

2010-01-18 Thread 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-correla

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

2010-01-17 Thread 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-correla