[gmx-users] Hydrogen bonding differences

[Kavyashree M]

Dear Sir,

Sure I will try with 4.6. presently I am not able to download it.

Thank you
kavya

On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> 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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