Problem with H-bond

User discussions
1

GROMACS version: 2023.1
GROMACS modification: Yes/No
Here post your question

I have problem when i want calculate a H-bond Protein-Protein

my cmd : gmx hbond -s md100.tpr -f md100_c.xtc -num hb100.xvg -tu ns -n index1.ndx

the xvg file is like this :

@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”
-1.58495e+29 -268433344 -268433344
4.56585e-41 32583 32583
-1.58495e+29 -268433344 -268433344
4.56585e-41 32583 32583
-1.61211e+29 -268064608 -268015440
4.56585e-41 32583 32583
-1.61211e+29 -268064608 -268015440
4.56585e-41 32583 32583
0 3660 9823
0 4086 6542
0 5215 11044
0 3796 9823
0 4045 6180
0 5418 11116
0 3609 9657
0 4412 5905
0 5418 10897
0 3609 9591
0 4412 10882
0 5992 9420
0 3614 5470
0 4896 10744
0 6211 9555
0 3273 5138
…
81.92 5 6998
81.93 5 6953
81.94 5 4885
81.95 5 6624
81.96 4 6625
81.97 4 5337
81.98 4 6766
81.99 3 10642
82 4 10157
82.01 4 3055
82.02 3 5931
82.03 3 5663
82.04 3 4128
82.05 4 10980

only from 81.92 ps I get the correct value

Can you help me

2

some remark:
I use the following command line

gmx hbond -s md.tpr -f md_c.xtc -num hb.xvg -tu ns -n index.ndx

I checked with the VMD program, the number of H-bonds is correct with this program.
so there is a problem with gromacs for determining the number

3

i am facing the same problem since two weeks but i did not find solution

4

What does gmx check tell you about md_c.xtc? Is md_c.xtc directly from mdrun or did you construct it in some way? If the latter, what did you do to write this file?

5

Thank you for your reply, i want to show you command that i have used to create the md_c.xtc for 100ns is:
“gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_10.tpr
gmx mdrun -deffnm md_0_10”
until now, I am following gromac tutorial.

6

Hi
I use the commande line of gromacs only

For all calculations like rmsd rmsf gyr sas all i have the correct value only with hbond that i have a problem
Withthe same file Xtc and gro by using VMD I have the correct value of HBond

1 Like
7

I would highly appreciate if you could help.

echo Backbone System | gmx trjconv -s md_sim.tpr -f md_sim.xtc -o md_sim_center.xtc -center -pbc mol -ur compact
echo Backbone System | gmx trjconv -s md_sim.tpr -f md_sim_center.xtc -o md_sim_fit.xtc -fit rot+trans

Simulation done with Gromacs 2023.1
H_Bond does not work (H_Bond_Gromacs-2023.1.xvg)
H_Bond_Gromacs-2023.1.xvg (1.7 MB)

–
Command line:
gmx check -f md_sim_fit.xtc

Checking file md_sim_fit.xtc
Reading frame 0 time 0.000

Atoms 47456

Precision 0.001 (nm)
Last frame 50000 time 500000.000

Item #frames Timestep (ps)
Step 50001 10
Time 50001 10
Lambda 0
Coords 50001 10
Velocities 0
Forces 0
Box 50001 10
**

Simulation done with Gromacs 2022
H_Bond works fine (H_Bond_Gromacs-2022.xvg)
H_Bond_Gromacs-2022.xvg (1.7 MB)

–
Command line:
gmx check -f md_sim_fit.xtc

Checking file md_sim_fit.xtc
Reading frame 0 time 0.000

Atoms 47456

Precision 0.001 (nm)
Last frame 50000 time 500000.000

Item #frames Timestep (ps)
Step 50001 10
Time 50001 10
Lambda 0
Coords 50001 10
Velocities 0
Forces 0
Box 50001 10

8

There are memory issues in the 2023 and 2023.1 version of gmx hbond. This will be fixed in 2023.2. gmx hbond from version 2022 likely works.

9

hello. i am facing the same problem. any solution for this?