[gmx-users] troubles with eigenvectors

Ivano Eberini Ivano.Eberini at unimi.it
Fri Jan 11 12:20:09 CET 2002

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.
If we look at the filtered.xtc file with gmxdump, it seems to be OK.
This trouble happened both on a G4 running GROMACS version 3.0.99 and on 
a Red Hat Linux PIII running GROMACS 3.0.5.
I am almost sure we did a mistake, but I cannot understand which one.
Thanks in advance.

Best regards,
Ivano Eberini
Laboratorio di Farmacologia del Diabete
Dipartimento di Scienze Farmacologiche
Università degli Studi di Milano
Via G. Balzaretti, 9
20133 - Milano
Tel.: +39025835-8304/-8359 Fax: +390258358284


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