-[no]da flag in g_hbond is broken
-[no]da doesn't work. The two following commands generate identical results:
g_hbond ... -noda -r 0.25
g_hbond ... -da -r 0.25
It seems the donor acceptor distance is used at all times. The same problem
arises in gmx 3.3, 3.3.2b and in the 4.0 development code.
#5 Updated by Erik Marklund about 12 years ago
Oops, uploaded trajectory twice.
g_hbond -s grompp_run.tpr -f short.xtc -num da_num -g da_g -da
g_hbond -s grompp_run.tpr -f short.xtc -num noda_num -g noda_g -noda
da_num.xvg and noda_num.xvg were identical, apart from comments/quotes. It was all done with gmx version 4.0 and the AMBER03 force field.