[gmx-users] g_order in Gromacs 3.3.1
Arneh Babakhani
ababakha at mccammon.ucsd.edu
Wed May 31 17:43:55 CEST 2006
As have I. Very well, I have submitted a bugzilla (#84),
Arneh
Sukit Leekumjorn wrote:
> 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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