[gmx-users] Number of interactions per residue

Erik Marklund erikm at xray.bmc.uu.se
Tue Feb 19 11:44:59 CET 2013 

On Feb 19, 2013, at 10:19 AM, Kavyashree M wrote:

> Dear users,
>
> *When I use g_hbond with -contact and -r 0.4 on C-alpha atoms -*
> I get the following message -
> ***************************************************************************
> Reading frame       0 time 4000.000
> Will do grid-seach on 26x26x19 grid, rcut=0.4
> Last frame        500 time 5000.000
> Found 509 different contacts in trajectory
> Found 0 different atom-pairs within hydrogen bonding distance
> Merging hbonds with Acceptor and Donor swapped
> 474/474
> - Reduced number of hbonds from 509 to 509
> - Reduced number of distances from 0 to 0
> Average number of contacts per timeframe 0.000 out of 112338 possible
>
> -------------------------------------------------------
> Program g_hbond, VERSION 4.5.3
> Source code file: gmx_hbond.c, line: 4052
>
> Range checking error:
> Variable y has value 0. It should have been within [ 0 .. 0 ]
>
> For more information and tips for troubleshooting, please check the  
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> ***************************************************************************
>
> *With the option -contact -r2 0.4 on C-alpha atoms I get-*
> ****************************************************************************
> Reading frame       0 time 4000.000
> Will do grid-seach on 26x26x19 grid, rcut=0.4
> Last frame        500 time 5000.000
> Found 4 different contacts in trajectory
> Found 507 different atom-pairs within second cut-off distance
> Merging hbonds with Acceptor and Donor swapped
> 474/474
> - Reduced number of hbonds from 4 to 4
> - Reduced number of distances from 507 to 507
>
> *With the option -contact -r 0.35 -r2 0.4 on C-alpha atoms I get-*
> ****************************************************************************
> Reading frame       0 time 4000.000
> Will do grid-seach on 26x26x19 grid, rcut=0.4
> Last frame        500 time 5000.000
> Found 4 different contacts in trajectory
> Found 507 different atom-pairs within second cut-off distance
> Merging hbonds with Acceptor and Donor swapped
> 474/474
> - Reduced number of hbonds from 4 to 4
> - Reduced number of distances from 507 to 507
>
> The index and the matrix that it writes has only 4 contacts  
> (highlighted).
> Why is it says as Hbond?

That should read 'contacts'

> But isnt the "507" the number of contacts?

contacts within r2

> What is the 4 hbonds?
>
> What do I need to do If I want to get the C-alpha contacts in the form
> of a matrix, which gives the presence/absence of a contact over the
> entire simulation?
>
> Kindly help..
>
> Thank you
> Kavya
>
> On Tue, Feb 19, 2013 at 9:56 AM, Kavyashree M <hmkvsri at gmail.com>  
> wrote:
>
>> Sir,
>>
>> My purpose was to compare two simulations of the
>> same protein at different temperatures. So I wanted
>> to see how the interaction of each residue with other
>> residues, within a cut-off, varies between the two.
>> by using the matrix of C-alpha contact over the whole
>> trajectory.
>>
>> Thank you
>> kavya
>>
>>
>> On Tue, Feb 19, 2013 at 9:50 AM, Kavyashree M <hmkvsri at gmail.com>  
>> wrote:
>>
>>> Hello Sir,
>>>
>>> I used C-alpha atoms.
>>>
>>> Kavya
>>>
>>>
>>> On Mon, Feb 18, 2013 at 11:28 PM, Erik Marklund <erikm at xray.bmc.uu.se 
>>> >wrote:
>>>
>>>> Hi,
>>>>
>>>> With -r2 one can provide a second, larger, cutoff so that contact
>>>> kinetics can be analyzed within the Luzar-Chandler framework that  
>>>> were
>>>> designed for hbonds.
>>>>
>>>> What index groups did you use?
>>>>
>>>> Erik
>>>>
>>>>
>>>> On Feb 18, 2013, at 6:04 PM, Kavyashree M wrote:
>>>>
>>>> Dear users,
>>>>>
>>>>> As Suggested by Erik, I used g_hbond with -contact  to obtain a  
>>>>> matrix
>>>>> of
>>>>> each contact as a function of time. I used the following command -
>>>>> g_hbond -f a.xtc -s a.tpr -contact -r2 0.5 -hbm m.xpm -b 4000 -e  
>>>>> 4400
>>>>> -hbn
>>>>> c.ndx
>>>>>
>>>>> I get only three contacts in the index file. The protein is a  
>>>>> dimer of
>>>>> 474
>>>>> residues
>>>>> (237 each). With a distance cut off of 0.5nm there should have  
>>>>> been more
>>>>> number
>>>>> of contacts. And what is the difference in using -r only or -r2  
>>>>> only and
>>>>> combining -r
>>>>> and -r2?
>>>>>
>>>>> Thank you
>>>>> Kavya
>>>>>
>>>>> On Thu, Feb 14, 2013 at 3:40 PM, Kavyashree M <hmkvsri at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Thank you!
>>>>>>
>>>>>>
>>>>>> On Thu, Feb 14, 2013 at 3:38 PM, Erik Marklund <erikm at xray.bmc.uu.se
>>>>>>> wrote:
>>>>>>
>>>>>> Perhaps g_hbond -contact will do what you want.
>>>>>>>
>>>>>>> Erik
>>>>>>>
>>>>>>>
>>>>>>> On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote:
>>>>>>>
>>>>>>> Dear users,
>>>>>>>
>>>>>>>>
>>>>>>>> How can I get the number of interactions of each residue
>>>>>>>> within a cut off as a function of time. just like g_saltbr  
>>>>>>>> writes
>>>>>>>> with the option -sep.
>>>>>>>> I tried using g_mdmat but it gives an average contact map.
>>>>>>>>
>>>>>>>> Thank you
>>>>>>>> Kavya
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