[gmx-users] g_order in Gromacs 3.3.1

Sukit Leekumjorn leekumjo at vt.edu
Mon May 8 17:24:05 CEST 2006

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.


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
         -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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