Hi Aiman Parvez ,

From your hbond.xvg file, I can see that your command line was:

gmx hbond -s em.tpr -f md_0_1_center.xtc -n index.ndx -num hbond.xvg

I believe you might have specified the wrong .tpr file.

Make sure to select the tpr file generated after the production run and in your case, I'm assuming it is something like md_0_1.tpr or md_0_1_center.tpr

You should get better hydrogen bond results once you input the right tpr file.

Hope this helps. All the best.

i have use this command but the same problem

gmx hbond -s md_0_1.tpr -f md_0_1_center.xtc -n index.ndx -num hbond.xvg

i dont know what is the main problem

can you please help me to sort it out.