Hi,
With -r2 one can provide a second, larger, cutoff so that contact
kinetics can be analyzed within the Luzar-Chandler framework that were
designed for hbonds.
What index groups did you use?
Erik
On Feb 18, 2013, at 6:04 PM, Kavyashree M wrote:
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 <hmkv...@gmail.com>
wrote:
Thank you!
On Thu, Feb 14, 2013 at 3:38 PM, Erik Marklund
<er...@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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