Re: [gmx-users] g_order in Gromacs 3.3.1

Wed, 31 May 2006 05:16:04 -0700 

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:


_______________________________________________
gmx-users mailing list    gmx-users@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 [EMAIL PROTECTED] 
Can't post? Read http://www.gromacs.org/mailing_lists/users.php




_______________________________________________
gmx-users mailing list    gmx-users@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 [EMAIL PROTECTED] 
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



_______________________________________________
gmx-users mailing list    gmx-users@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 [EMAIL PROTECTED] 
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to