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 <er...@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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