[gmx-users] Number of interactions per residue

[Kavyashree M]

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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