[gmx-users] h-bonds by g_hbond and VMD and ptraj

Ondrej Kroutil okroutil at gmail.com
Fri Oct 2 17:39:10 CEST 2015

Hi gromacs users.
I did h-bond analysis between solute and solvent using g_hbond utility with
default settings (3.5A, 30°) and same analysis in VMD (Hydrogen bonds
module) with same settings. And I get different numbers. So I did same
analysis with cpptraj from Amber (angle 150° due to different definition of
h-bond angle criterion) and I get same results as in VMD (see table below).
Differences were even larger for distance 3.0A and angle 20°. So I tried
different versions of Gromacs and results were same in all three versions.

                                         nr. of h-bonds
Grom (5.0), 3.5A, 30deg          9.343
Grom (5.0.5), 3.5A, 30deg       9.343
Grom (4.5.3), 3.5A, 30deg       9.343
VMD, 3.5A, 30deg                  8.617
cpptraj, 3.5A, 150deg              8.617

Grom (5.0), 3.0A, 20deg          6.294
VMD, 3.0A, 20deg                  4.317
cpptraj, 3.0A, 160deg              4.318

For g_hbond I used this command:

g_hbond_gpu -s topol.tpr -f center-15.000.xtc -n index.ndx -a 30 -r 0.35
g_hbond_gpu -s topol.tpr -f center-15.000.xtc -n index.ndx -a 20 -r 0.30

Please, do you have any suggestions why I get different numbers from
g_hbond compared to VMD and cpptraj???

Thank you very much and enjoy upcoming weekend.

  Ondrej Kroutil

Ondřej Kroutil
        ,,              Faculty of Health and Social Studies
   ----"))'             University of South Bohemia
     OOO           Jirovcova 24, Ceske Budejovice
      OOO          The Czech Republic
        | OO         E-mail:  okroutil at gmail.com
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