Jamie Seyed wrote:
On Mon, Aug 24, 2009 at 3:44 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Jamie Seyed wrote:
with a lot of x-y sets seperated by & character. I think I did
not get the key point here. So my question is what is the right
way to get <R(0)R(t)> using this tool?? Many Thanks/Jamie
Well, as far as g_analyze is concerned, it's done its job. If you
feed g_analyze a whole bunch of data sets, it will give you a whole
bunch of ACF's. So you essentially got an ACF for each molecule's x,
y, and z coordinates. I guess I just don't understand what you're
really after, because as I said, g_analyze did its job.
Thanks a lot Justin,
Actually I tried to use xmgrace to make a <> of all bunch of ACF and I
find under data/feature extraction/Feature Y average to do the job. I
did not find out how it works yet, but do you think is this correct??
I think, if you average the ACF, you will get zero.
--another question related to g_rotacf. Before I used it like this:
first I made a ndx file and then extract xtc and tpr file for ndx and
then used this command:
1) g_rotacf -f f.xtc -s tpxout.tpr -n f.ndx -o rotacf.xvg -d
and I saw strange result (as I mentioned before like y=2x)
Then I tried to use original files (xtc and tpr) insted of filtered files:
2) g_rotacf -f traj.xtc -s f.tpr -n f.ndx -o rotacf.xvg -d
and I got completely different but very expected result. So now I
believe that the right way is the second one... Do you have any idea or
comment on this? or what is the result of first method?
Filtered trajectories are for visualization purposes only. When doing analysis,
always use the original trajectory.
-Justin
Many Thanks/Jamie
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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