Jamie Seyed wrote:
Hi Justin and Mark,
Thanks. Actually I made a mistake and it seems going to the zero (even
negative!)
--But I wanted to know how I can write my command to get only one graph
(average of all instead of all of them). I read the manual chapter-8 and by
average I mean I should get one curve starting at 1 and coming down to
zero...I also tried
g_analyze -f coord.xvg -ac autocorr.xvg -av average.xvg
but I do not know what is this average file (it is not clearly what I am
looking for).
We can't know either, because you haven't told us what you're looking
for. Read "g_analyze -h", of course.
--Also for the same purpose I tried g_rotacf -d ,
first I extract the coordinates of selected atoms into f.xtc and then tried
this command:
g_rotacf -f f.xtc -s f.tpr -n f.ndx -o retacf.xvg -d
I got an error message that : " Molecule in topology has atom numbers below
and above natoms. you are
probably trying to use a trajectory which does not match the first 330 atoms
of the run input file. You can make a matching run input file with *tpbconv*
."
But when I used tpbconb to generate new tpr file using my index file,
without giving an error it says "0 steps (0 ps) remaining from first run.
You have simulated lon enough. not writing tpr file" and nothing has been
generated.
Read "tpbconv -h". There are multiple uses for tpbconv, and it looks
like the order of the error-checking is inconvenient for your situation.
So use -extend arbitrarily. You're not using this file for simulation,
so that doesn't matter.
I read this problem from mailing list and people said that I can use pdb/gro
file instead. So I modified last gro file and kept the same atoms as my
index file (ref.gro) and used it instead of tpr file:
g_rotacf -f f.xtc -s ref.gro -n f.ndx -o retacf.xvg -d
But Can not open ref.gro.tpr
So I do not know how to get rid of this error...Thanks in Advance/Jamie
Some analysis tools will accept any structure file, and some require a
run input file. Look at the acceptable file types for -s in "g_rotacf -h".
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
