lammps lammps wrote:
Hello everyone,
I use the g_order to get the order parameter of the tails( C1A, C2A,
C3A, C4A) of DPPC. The are 100 molecules of DPPC
1. I use the make_ndx -f dppc.trr -n index to produce the index file.
> a C1A
> a C2A
> a C3A
> a C4A
> del 0-3
Q_1: Is the method right to produce the index file?
There is a how-to on the g_order page:
http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order
Your procedure seems like it might be right, but what are atoms C1A, C2A, etc?
This isn't the numbering I'm used to. What are groups 0-3?
Then there only four groups orderly named C1A, C2A, C3A, C4A in the
index file.
2. I use the g_order -n index -s npt.tpr ... to get the order parameter.
However, there are lots of errors
Don't use "..." when posting a command. Provide the whole command.
.........
WARNING: distance between atoms 29777 and 29779 > 0.3 nm (0.897513).
Index file might be corrupt.
WARNING: distance between atoms 29789 and 29791 > 0.3 nm (0.709495).
Index file might be corrupt.
WARNING: distance between atoms 29801 and 29803 > 0.3 nm (0.692954).
Index file might be corrupt.
WARNING: distance between atoms 29813 and 29815 > 0.3 nm (0.784918).
Index file might be corrupt.
WARNING: distance between atoms 29825 and 29827 > 0.3 nm (0.839048).
Index file might be corrupt.
WARNING: distance between atoms 29837 and 29839 > 0.3 nm (0.851105).
Index file might be corrupt.
WARNING: distance between atoms 29849 and 29851 > 0.3 nm (0.790752).
Index file might be corrupt.
WARNING: distance between atoms 29861 and 29863 > 0.3 nm (0.836583).
Index file might be corrupt.
WARNING: distance between atoms 29873 and 29875 > 0.3 nm (0.854105).
Index file might be corrupt.
WARNING: distance between atoms 29885 and 29887 > 0.3 nm (0.847901).
Index file might be corrupt.
WARNING: distance between atoms 29897 and 29899 > 0.3 nm (0.758556).
Index file might be corrupt.
...........
Why?
These messages seem to indicate that you have non-sequential carbon atoms.
Cross-check the atom names you've used to create the index file with the actual
coordinates.
-Justin
3. Result
Last frame 4 time 240.000
Read trajectory. Printing parameters to file
Atom 1 Tensor: x=-0.267416 , y=-0.245994, z=0.51341
Atom 2 Tensor: x=-0.207203 , y=-0.171233, z=0.378436
Back Off! I just backed up order.xvg to ./#order.xvg.1#
Back Off! I just backed up deuter.xvg to ./#deuter.xvg.1#
gcq#51: "The Stingrays Must Be Fat This Year" (Red Hot Chili Peppers)
[tia...@localhost dppcden5]$ cat order.xvg
# This file was created Sun Apr 23 10:10:35 2006
# by the following command:
# g_order -f traj.trr -n index.ndx -s npt.tpr -o -e 240
#
# g_order is part of G R O M A C S:
#
# Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
#
@ title "Order tensor diagonal elements"
@ xaxis label "Atom"
@ yaxis label "S"
@TYPE xy
1 -0.267416 -0.245994 0.51341
2 -0.207203 -0.171233 0.378436
[tia...@localhost dppcden5]$
--
wende
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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
