[gmx-users] g_hbond and contact

[Kavyashree M]

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?

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?

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
>
>