g_velacc g_dos do not match
there are several issues with g_dos and g_velacc.
1. they both do not accept "-n" as they should;
2. g_dos does not accept "-normalize";
3. The output of g_velacc, i.e. -o vel.xvg -os spec1.xvg
do not match that of g_dos, i.e. -vacf vel.xvg -dos spec.xvg, respectively;
4. The g_dos .log file has some errors.
Fix bugs in gmx dos
- Velocity autocorrelations were not normalized
by default, so they did not agree with gmx velacc.
- The normalize option had no effect on the VACs.
- The index group option was available, but no
index groups were processed.
- Since the DoS is calculated from the mass-weighted
VAC and by default only from the real part, it was
not clear why these results would differ from data
obtained with gmx velacc. There is at least a note
about this now, and more docs will be added in the
- The hidden option to dump some plots has been
removed since it was not documented what these
contained (beyond a paper reference), and the
contents was not based on any data from the
trajectory, but rather plotting a custom function.
#3 Updated by Erik Lindahl over 2 years ago
- Status changed from New to Fix uploaded
- Target version set to 5.0.6
The density-of-states tool appears to have been largely abandoned, and since it also produces velocity autocorrelations that do not agree with those of gmx velacc we should remove it until somebody wants to look into the tool and provide documentation and fixes.