[gmx-users] Number of interactions per residue

[Kavyashree M]

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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