[gmx-users] Hydrogen bonding differences

[Erik Marklund]

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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