[gmx-users] Number of interactions per residue

[Kavyashree M]

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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