aiswarya pawar wrote:
Hi everyone,
when am doing this g_dist between the protein and water am getting the
distance between water-water. why it is so?? and is there a way i can
find distance in each time frame.
The distance is calculated based on the groups you tell g_dist to analyze. If
you're getting water-water distances it's because either your index groups are
constructed incorrectly, you're telling g_dist to do this, or you're
misinterpreting the output.
-Justin
Thanks
On Thu, Sep 8, 2011 at 5:55 PM, aiswarya pawar <aiswarya.pa...@gmail.com
<mailto:aiswarya.pa...@gmail.com>> wrote:
Hi users,
To get the distance between water and protein i did -
g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11
from this i should obtain an output file as distance.xvg which i
dont get.
and my output is printed on the terminal as-
t: 1 136 SOL 2336 OW 0.772373 (nm)
t: 1 136 SOL 2337 HW1 0.706358 (nm)
t: 1 136 SOL 2338 HW2 0.807787 (nm)
t: 1 139 SOL 2345 OW 0.821094 (nm)
t: 1 139 SOL 2346 HW1 0.810919 (nm)
t: 1 139 SOL 2347 HW2 0.771526 (nm)
t: 1 7237 SOL 23640 HW1 0.997056 (nm)
t: 1 11793 SOL 37307 OW 0.868929 (nm)
t: 1 11793 SOL 37308 HW1 0.927205 (nm)
t: 1 11793 SOL 37309 HW2 0.776699 (nm)
t: 2 125 SOL 2303 OW 0.940527 (nm)
In this
t: 1 136 SOL 2336 OW 0.772373 (nm)
does the 't' states the time frame, 136 SOL states the SOL molecule
number and 2336 OW the residue contact from protein and the 0.772373
nm the distance between them.
Thanks
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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