[gmx-users] trjorder

[Justin Lemkul]

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

-- 
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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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