GROMACS version:2023.3
GROMACS modification: Yes/No
Hello everyone, I currently want to use the gmx hbond command to calculate hydrogen bonds between specified protein atom groups. First, I generated the specified atom groups using the command gmx make_ndx -f result.gro -o index.ndx. Then, I processed the trajectory file with gmx trjconv -f result.xtc -s md.tpr -o 40-50ns.xtc -b 40000 -e 50000 -pbc mol -center -ur compact to center the protein and save a 10ns trajectory file. Finally, I used the command gmx hbond -f 40-50ns.xtc -s md.tpr -n index.ndx -num -hbn -hbm to generate three files: hbmap.xpm, hbnum.xvg, and hbond.ndx. The hbmap.xpm and hbnum.xvg files are shown in the figures below. However, in the [ hbonds_Protein ] section of the hbond.ndx file, the specific atoms forming the hydrogen bonds are not correctly displayed, and the middle atom always shows an index of -1. Could anyone explain what might be causing this issue?
hbond.ndx:
hbnum.xvg:
