aiswarya pawar wrote:
Hi Justin,
Am using g_dist to find the distance between water and protein. for that i made
a index file such as-
a CA(protein atoms)
a OW(water atoms)
i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35
instead of getting the result for protein-SOL distance . my output shows SOL-OW
distance as seen below-
t: 1 136 SOL 2336 OW 0.772373 (nm)
even after specifying am getting an wrong output.
I don't know why this shows up if you're using "-dist 0.35" but it still sounds
like you're going about your task the wrong way. If you want the distance
between CA atoms and water as a function of time, leave off -dist and the output
you want is in the dist.xvg file written by g_dist (-o output option). This
will be a relatively insensitive measurement and you will probably need better
index groups.
-Justin
Thanks
On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
aiswarya pawar wrote:
Hi Users,
Am using g_dist to find the distance between water and protein.
but my output has the values of SOL-water distance.
t: 1 136 SOL 2336 OW 0.772373 (nm)
This is not a water-water distance, it is the output of the -dist
option telling you that water molecule 136 has its OW atom at
0.7723273 nm from whatever your reference group is.
-Justin
--
==============================__==========
Justin A. Lemkul
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ICTAS Doctoral Scholar
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Virginia Tech
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========================================
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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