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
On Mar 5, 2013, at 5:20 AM, Kavyashree M wrote:
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 how many
contacts each
atom has from both S1 and S2.
2. -num output graph was compared from both S1 and S2.
g_mdmat output: of "-no" was considered.
3. -no output was analysed from both S1 and S2 using the
third column or the second Y value which gives total
contacts
of each atom.
It was observed that "1" and "3" matched exactly giving the same
number of
contacts each atom has (in the whole simulations). indicating that the
number
of contacts each atom has was more in S2 than S1.
But the graph from "2" indicated that the number of contacts (along
the
trajectory)
in S1 was higher than S2.
My doubt is:
The number of contact per atom follows S2 > S1
while number of contacts per time follows S1 > S2.
I am unclear as to what I have to conclude from this observations.
-----> I used the same cutoff throughout.
-----> There has not been any swapping of the trajectory while
analysing.
Thank you
Kavya
On Tue, Mar 5, 2013 at 1:09 AM, Justin Lemkul <jalem...@vt.edu> wrote:
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 group of hydrophobic atoms in both cases
The command I gave -
g_hbond_46 -f x.xtc -s x.tpr -contact -n x.ndx -
r 0.4
-hbm o.xpm -hbn o.ndx -num o.xvg
my index file contained a group of hydrophobic atoms. which I
supplied in
the x.ndx.
You don't define contacts in an index group, you define atoms
that may
or
may not make contacts with others.
The one I mentioned here is the output index file from the
g_hbond (4.6
version) - o.ndx.
[ contacts_C_CA_CB_CD_CD1_CD2_****CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_***
*CZ2_CZ3_CH2
]
5 7ws
5 10
5 14
5 18
5 22
5 24
5 27
5 30
5 35
5 292
5 296
5 30
There's something very wrong with this index file. How did you
generate
it? The presence of a repeated atom number (5) and a nonsensical
one
(7ws)
leads me to believe that you've done something incorrect. Did
this come
from g_hbond? It looks like the output of -hbn, which is only
useful for
decoding hbmap.xpm, nothing else.
I did not generate this. The tool (g_hbond) generated this index
file.
It
is the -hbn output.
OK, then I still don't know what "7ws" is, but the only purpose for
this
file is to provide a key to the existence matrix in hbmap.xpm. Your
previous description indicated that you were using it for some other
analysis, which would not be appropriate.
The other thing worth mentioning here is something that was posted
to the
list just a few hours ago, that the output of g_hbond -contact may
not
agree with other methods of calculating contacts, especially in the
case of
-merge vs. -nomerge.
-Justin
From this second section Total contacts was extracted for each
atom and
compared with
that from a second simulation.
These contacts was matching with the contacts of the 3rd column
from
g_mdmat output -
@ legend string 0 "Total/mean"
@ legend string 1 "Total"
@ legend string 2 "Mean"
@ legend string 3 "# atoms"
@ legend string 4 "Mean/# atoms"
#res ratio tot mean natm mean/atm
1 1.001 11 10.991 1 10.991
2 1.244 10 8.041 1 8.041
3 1.166 13 11.147 1 11.147
4 1.036 11 10.615 1 10.615
While the time dependent contacts in the xvg file shows that the
first
simulation has more
contacts than the second one..
That shouldn't be unexpected. Two independent simulations have no
guarantee of doing the same thing, that's why sampling is so
important.
Thank you
kavya
--
==============================**==========
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
==============================**==========
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