FYI, the bug in g_order has been resolved, see:
http://bugzilla.gromacs.org/show_bug.cgi?id=84
for details.
Sukit Leekumjorn wrote:
Dear GMX users,
I have encounter some problem with g_order in Gromacs3.3.1. I noticed
that tetrahedral order parameter has been added to the new version and
for some reason, the program seems to call for calc_tetra_order_parm
loop rather than calculate regular tail order parameter. For
Gromacs3.3, the order parameter calculates normally. Below is the run
from g_order in 3.3.1. It stops at "Select a group" and nothing
proceed afterward when it should have picked the listed atoms (group 0
to 17) and started the calculation. I did put group 0 and the program
started to calculate and it gave sg-ang.xvg and sk-dist.xvg as the
outputs.
Sukit
g_order_3.3.1_s -f 4palmmdruncombine.xtc -s 4palmmdrun1.tpr -n
4palmmdrun_sn1.ndx -od test.xvg -e 100
:-) G R O M A C S (-:
GROningen MAchine for Chemical Simulation
:-) VERSION 3.3.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2006, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_order_3.3.1_s (-:
Option Filename Type Description
------------------------------------------------------------
-f 4palmmdruncombine.xtc Input Generic trajectory: xtc trr
trj gro
g96 pdb
-n 4palmmdrun_sn1.ndx Input Index file
-s 4palmmdrun1.tpr Input Generic run input: tpr tpb tpa xml
-o test.xvg Output xvgr/xmgr file
-od deuter.xvg Output xvgr/xmgr file
-os sliced.xvg Output xvgr/xmgr file
-Sg sg-ang.xvg Output xvgr/xmgr file
-Sk sk-dist.xvg Output xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line
options
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 100 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the
output
xvg files for the xmgrace program
-d enum z Direction of the normal on the membrane: z,
x or
y
-sl int 1 Calculate order parameter as function of
boxlength, dividing the box in #nr slices.
-[no]szonly bool no Only give Sz element of order tensor. (axis
can
be specified with -d)
-[no]unsat bool no Calculate order parameters for unsaturated
carbons. Note that this cannot be mixed with
normal order parameters.
Reading file 4palmmdrun1.tpr, VERSION 3.3 (double precision)
Reading file 4palmmdrun1.tpr, VERSION 3.3 (double precision)
Select the group that contains the atoms you want to use for the
tetrahedrality order parameter calculation:
Group 0 ( o15) has 144 elements
Group 1 ( o17) has 144 elements
Group 2 ( o18) has 144 elements
Group 3 ( o19) has 144 elements
Group 4 ( o20) has 144 elements
Group 5 ( o21) has 144 elements
Group 6 ( o22) has 144 elements
Group 7 ( o23) has 144 elements
Group 8 ( o24) has 144 elements
Group 9 ( o25) has 144 elements
Group 10 ( o26) has 144 elements
Group 11 ( o27) has 144 elements
Group 12 ( o28) has 144 elements
Group 13 ( o29) has 144 elements
Group 14 ( o30) has 144 elements
Group 15 ( o31) has 144 elements
Group 16 ( oa1) has 144 elements
Group 17 ( oa2) has 144 elements
Select a group:
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