[gmx-users] Do hydrogen bonds innately exist using mdrun?

James james at ryley.com
Fri Feb 8 23:20:41 CET 2019


I know that gromacs has an hbond command which will analyze hbonds after a
run. But, during a run, without doing something like specifying partial
charges, do hbonds exist?

It seems to me that they do not, because if I put two water molecules next
to each other, they do not assume the configuration they would if hbonds
were present, nor do the energies come out as expected (the affinity of the
two water molecules is 10X too low, which makes me think that gromacs is
using VDW, but ignoring hbonds).

I'd love to be wrong and find out that hbonds "just work"! But, if they do
not "just work," how do you specify them? I could see mimicking them by
tuning partial charges on the donor and acceptor atoms to give the correct
affinity, but it seems like that still would not be accurate because hbonds
are angle dependent, whereas long range non-bonded forces are not.

James Ryley, PhD, Patent Agent

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