[gmx-users] h-bonds by g_hbond and VMD and ptraj
erik.marklund at chem.ox.ac.uk
Mon Oct 5 01:07:37 CEST 2015
They use different angles to determine if it is a bond or not. See respective manuals.
Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College
Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
> On 2 Oct 2015, at 16:39, Ondrej Kroutil <okroutil at gmail.com> wrote:
> 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
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> | OO E-mail: okroutil at gmail.com
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