[gmx-users] g_order in Gromacs 3.3.1

[Arneh Babakhani]

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:
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>