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
========================================
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