Hi Pedro, thank you for your prompt reply.
I'm attempting to do what you suggested.
1). I create an index file, called sn2.ndx, which contains 14 groups,
one group for each carbon type in the chain (labeled C2A, C2B, . . . C2N).
2) I then try to execute the following command:
g_order -f FullMD10.trr -n sn2.ndx -s FullMD10.tpr -o order.xvg -od
deuter.xvg -os sliced.xvg
(in accordance with your suggestion, and what's posted in the g_order
manual).
I'm then asked to pick a group (from 0 to 13, corresponding to the 14
carbon types that are in the index file). So I assume then I have to
calculate the Scd of each carbon, one at a time? That's fine, I can
easily script that.
But when I pick a carbon, the following occurs:
Select a group: 0
Selected 0: 'C2A'
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.1#
Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1#
Last frame 1000 time 1000.000
gcq#195: "I Am a Poor Lonesome Cowboy" (Lucky Luke)
So the end result is a file called sg-ang.xvg and sk-dist.xvg. Why
didn't I get any of my output files (order.xvg, deuter.xvg, and
sliced.xvg) ???
Thanks again,
Arneh
[EMAIL PROTECTED] wrote:
Hello GROMACS community,
I was wondering if somebody could walk me through the process of
calculating lipid order parameters (for a DMPC membrane), using the
g_order analysis tool?
I've got a 5 ns trajectory and would like to make one of the classic
order parameter plots:
i.e.
On the y-axis: the order parameter averaged over the entire trajectory
On the x-axis: the Carbon number, or Carbon type (C2A on one tick, C2B
on the next tick, and so on . . . ).
I'm a little confused in how to set up the ndx file for this too.
Any help at all would be much appreciated!
Hello, Arneh.
1)First of all, you have to build an index.ndx (using make_ndx - see
manual)creating a group for each methylene and one for the methyl.
For instance, it will give [ C17 ], [ C18 ] ..., [ C29 ] groups, for
one tail of DMPC.
2)The index.ndx has to contain only this groups - you will have to
delete the others!
3)g_order -n index.ndx -od deuter.xvg will give you -Scd.
Regards.
Pedro.
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use thewww
interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
