[gmx-users] g_order in GMX4.05

[lammps lammps]

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?

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

.........
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?

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)
[tianwd at 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
[tianwd at localhost dppcden5]$


-- 
wende
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