[gmx-users] troubles with eigenvectors
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.
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