[gmx-users] Donors and Acceptors - gmx hbond

[Mark Abraham]

Hi,

I would use the selection groups judiciously, for example have one of them
with only donor atoms in it.

Mark

On Fri, 11 Aug 2017 00:05 Marcelo Depólo <marcelodepolo at gmail.com> wrote:

> Hi all!
>
>
> I've been wondering how donors and acceptors are defined in gmx hbond. In
> the help output:
>
> "(...) OH and NH groups are regarded as donors, O is an acceptor always, N
> is an acceptor by default, but this can be switched using -nitacc. Dummy
> hydrogen atoms are assumed to be connected to the first  preceding
> non-hydrogen atom.
>
> You need to specify two groups for analysis, which must be either identical
> or
> non-overlapping. All hydrogen bonds between the two groups are analyzed."
>
> So if I evaluate a 'OH' group (in MeOH - water solution, for example), will
> I be calculating the h-bonds donated by H atom and accepted by the O atom
> at the same time? If so, is there anyway to calculate both separately?
>
> Cheers!
> --
> Marcelo Depólo Polêto
> DSc. Cell and Molecular Biology - UFRGS (Brazil)
> Group of Structural Bioinformatics - Room 202
> Center of Biotechnology - UFRGS
> Phone: + 55 51 3308-7770
> --
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