[gmx-users] Hydrogen bonding differences

[Kavyashree M]

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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