[gmx-users] g_hbond and contact

[Erik Marklund]

On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote:

> Sir,
>
> I used gromacs 4.6. I got the point - index file will tell how many
> contacts an
> atom has made during the trajectory. Whether it has made a contact  
> with an
> atom only in once or all the time, in the whole trajectory, it will be
> mentioned.
> Am I right?

Yes.

>
> So from the problem I had, can I say that no. of contact/atom had  
> increased
> in S2 while the no. of contact/time decreased?

That depends. If 'contact' means unique interactions and 'atom' means  
e.g. all atoms in in your system, then yes.

>
> Its a bit confusing though!
>
> Thank you
> kavya
>
> On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund <erikm at xray.bmc.uu.se>  
> wrote:
>
>> To clarify: the -hbn output is not very indicative of how many  
>> contacts
>> there were since some of them could be present in one frame but  
>> absent in
>> 999999. The -num option, however, provides the number of contacts  
>> over
>> time, and its time average probably tells you much more in this case.
>>
>> What version of g_hbond are you using? I remember there were several
>> bugfixes over the last 6 months or so. With the latest version(s) I  
>> believe
>> that the -merge flag has no effect on contact analysis, which is  
>> correct.
>>
>> Erik
>>
>>
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