aiswarya pawar 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.
Try without specifying -dist simultaneously. Also realize that the distance
between the COM of the protein and the COM of water is probably constant (per
COM motion removal algorithms) and may actually be zero.
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.
More or less. OW, HW1, and HW2 are atoms, not residues. But yes, that's what
the -dist option does.
-Justin
--
========================================
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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