On 3/13/13 1:32 AM, Nidhi Katyal wrote:
Dear all
I would like to know the number of oxygen atoms of my co-solvent
molecules which are around 0.3nm of the protein in the last few ns. I
have read the manual and found that trjorder could serve the purpose.
So i have first created index file containing all the oxygen atoms of
my co-solvent molecules. Then I have used the following command:
trjorder -f *.xtc -s *.tpr -b 18000 -e 20000 -nshell nshell.xvg -na 1
Here I have used na as 1 since I am interested in number of atoms
instead of molecules (although one cosolvent molecule consists of 11
oxygen atoms).
Please guide me if I am proceeding in the right direction and if I am
wrong what na value should I give to serve the required purpose.
Why even bother with trjorder? g_dist -dist or use of g_select will give you
what you want without manipulating the trajectory in any way.
-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
========================================
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