[gmx-users] Number of interactions per residue

[Erik Marklund]

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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