[gmx-users] Hydrogen bonding differences

Kavyashree M hmkvsri at gmail.com
Mon Jan 21 10:55:29 CET 2013

Dear users,

While calculating hydrogen bonds for a simulation, it
was found that the average number of intra protein
hbonds was not equal to sum of MM, MS and SS
hydrogen bonds. (MM - main chain - main chain,
MS - main chain - side chain and side chain - side
chain hydrogen bonds). There was a difference of 5
or so hbonds between intra-protein and MM+MS+SS
hbonds. why is this so?
I selected the options 7 7 for MM, 7 8 for MS and 8 8
for SS hydrogen bonds.

One clarification. nhbdist option gives 0, 1, 2, 3 and
total hydrogen bonds per hydrogen. Does this mean
that a single hydrogen involving in forming hbond with
2 different acceptors/donors at different points of time
in the trajectory.


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