Hi, I have done a MD of a system GPCR/POPC, and I was trying to check my membrane with g_order. I made the index file like indicated in the web site using make_ndx -f md_0_10.tpr -o sn1.ndx
> 12 & a C15 | a C14 | a C6 | a C1 | a C2 | a C3 | a C5 | a C7 | a C4 | a C5 |
> a C7 | a C4 | a C8 | a C9 | a C10 | a C11 | a C12 | a C13 |
Copied index group 12 'POP'
Found 197 atoms with name C15
Merged two groups with AND: 10244 197 -> 197
Found 197 atoms with name C14
Merged two groups with OR: 197 197 -> 394
Found 197 atoms with name C6
Merged two groups with OR: 394 197 -> 591
Found 197 atoms with name C1
Merged two groups with OR: 591 197 -> 788
Found 197 atoms with name C2
Merged two groups with OR: 788 197 -> 985
Found 197 atoms with name C3
Merged two groups with OR: 985 197 -> 1182
Found 197 atoms with name C5
Merged two groups with OR: 1182 197 -> 1379
Found 197 atoms with name C7
Merged two groups with OR: 1379 197 -> 1576
Found 197 atoms with name C4
Merged two groups with OR: 1576 197 -> 1773
Found 197 atoms with name C5
Merged two groups with OR: 1773 197 -> 1773
Found 197 atoms with name C7
Merged two groups with OR: 1773 197 -> 1773
Found 197 atoms with name C4
Merged two groups with OR: 1773 197 -> 1773
Found 197 atoms with name C8
Merged two groups with OR: 1773 197 -> 1970
Found 197 atoms with name C9
Merged two groups with OR: 1970 197 -> 2167
Found 197 atoms with name C10
Merged two groups with OR: 2167 197 -> 2364
Found 197 atoms with name C11
Merged two groups with OR: 2364 197 -> 2561
Found 197 atoms with name C12
Merged two groups with OR: 2561 197 -> 2758
Found 197 atoms with name C13
Merged two groups with OR: 2758 197 -> 2955
16 POP_&_C15_C14_C6_C1_C2_C3_C5_C7_C4_C5_C7_C4_C8_C9_C10_C11_C12_C13: 2955
atoms
> del 0-15
Removed group 0 'System'
Removed group 1 'Protein'
Removed group 2 'Protein-H'
Removed group 3 'C-alpha'
Removed group 4 'Backbone'
Removed group 5 'MainChain'
Removed group 6 'MainChain+Cb'
Removed group 7 'MainChain+H'
Removed group 8 'SideChain'
Removed group 9 'SideChain-H'
Removed group 10 'Prot-Masses'
Removed group 11 'Non-Protein'
Removed group 12 'POP'
Removed group 13 'SOL'
Removed group 14 'CL-'
Removed group 15 'Other'
> q
then I use g_order
g_order -s md_0_10.tpr -f md_0_10.trr (or .xtc try both) -n sn1.ndx -d z -od
deuter_sn1.xvg
the program seems to read the trajectory
:-) G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
:-) VERSION 4.0.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, 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 (-:
Option Filename Type Description
------------------------------------------------------------
-f md_0_10.trr Input Trajectory: xtc trr trj gro g96 pdb cpt
-n sn1_check.ndx Input Index file
-s md_0_10.tpr Input Run input file: tpr tpb tpa
-o order.xvg Output xvgr/xmgr file
-od deuter_sn1_check.xvg Output xvgr/xmgr file
-os sliced.xvg Output xvgr/xmgr file
-Sg sg-ang.xvg Output, Opt. xvgr/xmgr file
-Sk sk-dist.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 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.
Taking z axis as normal to the membrane
Reading file md_0_10.tpr, VERSION 4.0.3 (single precision)
Using following groups:
Groupname: POP_&_C15_C14_C6_C1_C2_C3_C5_C7_C4_C5_C7_C4_C8_C9_C10_C11_C12_C13
First atomname: C15 First atomnr 2757
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000 Number of elements in first group: 2955
Last frame 5000 time 10000.000
Read trajectory. Printing parameters to file
but when I try to look at the results I only see
# This file was created Fri Jul 17 14:53:20 2009
# by the following command:
# g_order -s md_0_10.tpr -f md_0_10.trr -n sn1_check.ndx -d z -od
deuter_sn1_check.xvg
#
# g_order is part of G R O M A C S:
#
# Green Red Orange Magenta Azure Cyan Skyblue
#
@ title "Deuterium order parameters"
@ xaxis label "Atom"
@ yaxis label "Scd"
@TYPE xy
There no number. It is like nothing happen. I didn't had that issu for the rmsd
calculation or even density. I have a nice plot for both
Could somebody help me on that?
thank you in advance
Sabine
Dr. THIELGES Sabine
Associate Research Officer
Conseil national de recherches du Canada - National Research Council
Institut de recherche en biotechnologie - Biotechnology Research Institute
6100, avenue Royalmount, Montréal, Québec, H4P 2R2
tél: (514) 496-6255
sabine.thiel...@cnrc-nrc.gc.ca
<<winmail.dat>>
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