Check the input files: Ensure that the input files (md.tpr and md_center.xtc) are correct and properly formatted. If you haven't already, you should center and image the trajectory before calculating hydrogen bonds:

gmx trjconv -s md.tpr -f md.xtc -o md_center.xtc -center -ur compact -pbc mol

Alireza Mohebbi

Thank you for your response.

I checked all this again, and I still have the same error. Although I analyzed the RMSD, RMSF, Rg and SASA successfully.

Lotfi Bourougaa

I faced the same type of issue in hydrogen bond analysis. I analyzed the RMSD, RMSF, Rg and SASA successfully but not the hbond.

It shows like this:

@ title "Hydrogen Bonds"

@ xaxis label "Time (ps)"

@ yaxis label "Number"

@TYPE xy

@ view 0.15, 0.15, 0.75, 0.85

@ legend on

@ legend box on

@ legend loctype view

@ legend 0.78, 0.8

@ legend length 2

@ s0 legend "Hydrogen bonds"

@ s1 legend "Pairs within 0.35 nm"

1.44151e+17 1543505984 1543505936

4.56599e-41 32584 32584

1.44151e+17 1543505984 1543505936

4.56599e-41 32584 32584

1.48138e+17 1543819968 1543901904

4.56599e-41 32584 32584

1.48138e+17 1543819968 1543901904

4.56599e-41 32584 32584

1.44151e+17 0 0

4.56599e-41 0 0

1.44151e+17 0 0

4.56599e-41 0 0

1.48139e+17 0 0

4.56599e-41 0 0

1.48139e+17 0 0

4.56599e-41 0 0

5.13015e-42 0 0

2.49151e-42 0 0

-nan 0 0

5.22824e-42 0 0

2.20144e-42 0 0

-nan 0 0

5.40481e-42 0 0

2.40463e-42 0 0

-nan 0 0

5.51551e-42 0 0

2.85444e-42 0 0

2.05711e-42 0 0

-nan 0 0

8.06307e-42 0 0

1.95341e-42 0 0

I don't know exactly the reason. I think this is version issue.

Ankur Chaudhuri

You can solve this problem via VMD.

Lotfi Bourougaa

Thank you very much. Could you please tell me step?

Lotfi Bourougaa

Solved this issue by using vmd. But, sometime h-bond occupancy shows more than 100%. How is it possible?

Ankur Chaudhuri

Maybe you need to specify the frames.

Ankur Chaudhuri How do you solve the problem in VDM?