[gmx-users] g_hbond and contact

[Kavyashree M]

Thank you Sir.

On Tue, Mar 5, 2013 at 4:33 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

>
> 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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