Javier Cerezo wrote:
Hello
I tried to run g_order on a cluster with Core 2 Quad Q6600 processor
where the Gromacs Suite 4.0.1 has been compiled in single precision. The
program stops with a message from the compiler (i.e. in Spanish):
"Violación de segmento" (=Segmentation fault, I guess) and I couldn't
find an answer neither in the manual nor in the web. The program is run
with default parameters on a simulation of a membrane (the index.ndx
contains the membrane and the waters). Below, you can find the output.
Could someone give a clue about the problem and what to do?
Your index file is wrong. See here:
http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order
-Justin
Thanks a lot for your help.
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:-) g_order (-:
Option Filename Type Description
------------------------------------------------------------
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-n index.ndx Input Index file
-s topol.tpr Input Run input file: tpr tpb tpa
-o order.xvg Output xvgr/xmgr file
-od deuter.xvg Output xvgr/xmgr file
-os sliced.xvg Output xvgr/xmgr file
-Sg sg-ang.xvg Output, Opt. xvgr/xmgr file
-Sk sk-dist.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit -nice int
19 Set the nicelevel -b time 0 First frame
(ps) to read from trajectory
-e time 0 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.
Taking z axis as normal to the membrane
Reading file topol.tpr, VERSION 4.0.7 (single precision)
Using following groups: Groupname: DMPC
First atomname: C33 First atomnr 0 Groupname: SOL First atomname: OW
First atomnr 5888
Reading frame 0 time 0.000 Number of elements in first group:
5888
Reading frame 1 time 0.500 Violación de segmento
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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