[gmx-users] Hydrogen bonding differences

[Kavyashree M]

Sir,

I tried -nomerge. It is fine now. But will it be wrong to
calculate without nomerge option?

Thank you
Kavya

On Fri, Mar 22, 2013 at 9:28 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> I could see how -merge (on by default) could lead to this. Have you tried
> -nomerge?
>
> Erik
>
>
> On Mar 22, 2013, at 4:46 PM, Kavyashree M wrote:
>
>  Dear Users,
>>
>> As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds.
>> Still the
>> Total intra-protein hydrogen bonds is not equal (MM +MS +SS) hydrogen
>> bond.
>> Is there any other solution?
>>
>> Thank you
>> Kavya
>>
>> On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
>>
>>  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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