[gmx-users] Hydrogen bonding differences

[Erik Marklund]

Hi. What version was this? Have you tried with -nomerge?

Erik

On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:

> 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.
>
> Thanks
> kavya
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