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 atoms in those
two groups.
[ 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
You don't define contacts in an index group, you define atoms that may or may
not make contacts with others.
[ 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.
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.
-Justin
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
