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 99. The -num option, however, provides the number of
contacts over time, and its time average probably tells you much more
in this case.
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
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.
Thank you Sir.
On Tue, Mar 5, 2013 at 4:33 PM, Erik Marklund er...@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
On 3/4/13 11:25 AM, Kavyashree M wrote:
Dear users,
I used the following tool for finding the contacts
g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx
-num a.xvg
From the index file, the number of contacts of each atom was extracted.
This and the
xvg output was
Sir,
From Index file which gives the unique contacts -
First section the list of atoms I want to analyse
[ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]
second section : the unique contacts of each atoms with others
[
On 3/4/13 12:04 PM, Kavyashree M wrote:
Sir,
From Index file which gives the unique contacts -
First section the list of atoms I want to analyse
When measuring contacts, you don't measure one group, you measure the number of
contacts that occur between groups A and B, which considers all
On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote:
When measuring contacts, you don't measure one group, you measure the
number of contacts that occur between groups A and B, which considers all
atoms in those two groups.
I gave a group of hydrophobic atoms in both cases
On 3/4/13 1:10 PM, Kavyashree M wrote:
On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote:
When measuring contacts, you don't measure one group, you measure the
number of contacts that occur between groups A and B, which considers all
atoms in those two groups.
I gave a
I am sorry There is no 7ws Its a typographic error. What I wanted to ask
was -
I am comparing two simulations S1 and S2 for contacts at a given cut off
I used g_mdmat and g_hbond to calculate it.
g_hbond outputs: of -num and -hbn was considered.
1. -hbn output was analysed to calculate
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