On Feb 19, 2013, at 10:19 AM, Kavyashree M wrote:
Dear users,
*When I use g_hbond with -contact and -r 0.4 on C-alpha atoms -*
I get the following message -
***************************************************************************
Reading frame 0 time 4000.000
Will do grid-seach on 26x26x19 grid, rcut=0.4
Last frame 500 time 5000.000
Found 509 different contacts in trajectory
Found 0 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
474/474
- Reduced number of hbonds from 509 to 509
- Reduced number of distances from 0 to 0
Average number of contacts per timeframe 0.000 out of 112338 possible
-------------------------------------------------------
Program g_hbond, VERSION 4.5.3
Source code file: gmx_hbond.c, line: 4052
Range checking error:
Variable y has value 0. It should have been within [ 0 .. 0 ]
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
***************************************************************************
*With the option -contact -r2 0.4 on C-alpha atoms I get-*
****************************************************************************
Reading frame 0 time 4000.000
Will do grid-seach on 26x26x19 grid, rcut=0.4
Last frame 500 time 5000.000
Found 4 different contacts in trajectory
Found 507 different atom-pairs within second cut-off distance
Merging hbonds with Acceptor and Donor swapped
474/474
- Reduced number of hbonds from 4 to 4
- Reduced number of distances from 507 to 507
*With the option -contact -r 0.35 -r2 0.4 on C-alpha atoms I get-*
****************************************************************************
Reading frame 0 time 4000.000
Will do grid-seach on 26x26x19 grid, rcut=0.4
Last frame 500 time 5000.000
Found 4 different contacts in trajectory
Found 507 different atom-pairs within second cut-off distance
Merging hbonds with Acceptor and Donor swapped
474/474
- Reduced number of hbonds from 4 to 4
- Reduced number of distances from 507 to 507
The index and the matrix that it writes has only 4 contacts
(highlighted).
Why is it says as Hbond?
That should read 'contacts'
But isnt the "507" the number of contacts?
contacts within r2
What is the 4 hbonds?
What do I need to do If I want to get the C-alpha contacts in the form
of a matrix, which gives the presence/absence of a contact over the
entire simulation?
Kindly help..
Thank you
Kavya
On Tue, Feb 19, 2013 at 9:56 AM, Kavyashree M <hmkv...@gmail.com>
wrote:
Sir,
My purpose was to compare two simulations of the
same protein at different temperatures. So I wanted
to see how the interaction of each residue with other
residues, within a cut-off, varies between the two.
by using the matrix of C-alpha contact over the whole
trajectory.
Thank you
kavya
On Tue, Feb 19, 2013 at 9:50 AM, Kavyashree M <hmkv...@gmail.com>
wrote:
Hello Sir,
I used C-alpha atoms.
Kavya
On Mon, Feb 18, 2013 at 11:28 PM, Erik Marklund <er...@xray.bmc.uu.se
>wrote:
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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