[gmx-users] Hydrogen bonding differences

[Erik Marklund]

There were a handful of bugfixes to g_hbond over the last year. Could  
you try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form  
before.

Erik

On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote:

> Dear Sir,
>
> This is 4.5.3. I have not tried nomerge. I did not use
> nomerge option in any of them, So if it has counted
> it (Hbond b/w same donor and acceptor but with
> different hydrogen) twice in one calculation then it will
> be counted twice in another, So wont the result with/without
> nomerge be the same?
>
> The difference is 4-5 Hbonds..
>
> Thank you
> Kavya
>
> On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund  
> <erikm at xray.bmc.uu.se> wrote:
>
>> 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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>>
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