[gmx-users] troubles with eigenvectors

David van der Spoel spoel at xray.bmc.uu.se
Sat Jan 12 20:30:56 CET 2002

On Fri, 11 Jan 2002, Ivano Eberini wrote:

>we are trying to view a trajectory file (.xtc) generated by g_anaeig. 
>After covariance analysis, performed using g_covar, we were wondering if 
>it could be possible to filter our MD trajectory file (.trr) to show 
>only the motion along the first eigenvector. We used this command:
>g_anaeig -f full.trr -s full.tpr -filt filtered.xtc -first 1 -last 1
>When we tried to view filtered.xtc with ngmx (ngmx -f filtered.xtc -s 
>full.tpr -n index.ndx), we could see just an empty box and we were not 
>able to select any index, because check-boxes were not displayed in 
>their usual position.
Have you done covariance analysis on all atoms? Otherwise your filtered
trajectory will contain a subset of the atoms only, and your tpr does not
match your filtered.xtc. 

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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