[gmx-users] g_order in Gromacs 3.3.1

[Arneh Babakhani]

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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