[gmx-users] g_order in Gromacs 3.3.1

[Sukit Leekumjorn]

Concerning the problem with g_order in Gromacs 3.3.1.

I did try fixing the problem as suggested, however, I could not get it 
to work.  In the mean time, I just use g_order from 3.3 version.

Sukit

Arneh Babakhani wrote:
> Prof. Van Der Spoel,
>
> Regarding your suggestion here:  Where exactly are lines 579 and 580 
> that one must modify?  (I'm having this same error)
>
> Thanks,
>
> Arneh
>
> David van der Spoel wrote:
>> 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
>>
>> Thanks.
>>
>> At lines 579 and 580 replace the calls to opt2fn by opt2fn_null
>>
>>
>>>
>>> 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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>>
>>
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