[gmx-users] troubles with eigenvectors

[David van der Spoel]

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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