[gmx-users] Donors and Acceptors - gmx hbond

[Marcelo Depólo]

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