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

[Ondrej Kroutil]

Hi Erik,

Thank you for fast reply.
I knew about differences between definitions of angle criterion in Gromacs,
VMD and cpptraj but I didn't realize that there is nontrivial relationship
between these two different definitions.
I have gone deeper into this problem and now it makes sence to me.

Thank you.

    Ondřej Kroutil

On Mon, Oct 5, 2015 at 1:07 AM, Erik Marklund <erik.marklund at chem.ox.ac.uk>
wrote:

> Hi Ondrej,
>
> They use different angles to determine if it is a bond or not. See
> respective manuals.
>
> Kind regards,
> Erik
>
> Erik Marklund, PhD
> Postdoctoral Research Fellow
> Fulford JRF, Somerville College
>
> Department of Chemistry
> Physical & Theoretical Chemistry Laboratory
> University of Oxford
> South Parks Road
> Oxford
> OX1 3QZ
>
> > 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
> >     OOO           Jirovcova 24, Ceske Budejovice
> >      OOO          The Czech Republic
> >        | OO         E-mail:  okroutil at gmail.com
> >> ------    O         Mobile:  +420 736 537 190
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-- 
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
>------    O         Mobile:  +420 736 537 190