You may have defined position restraints that exceed the number of atoms
present your system, or define them in a wrong manner.
Check manual and previous posts.
On Apr 15, 2009, at 12:29 AM, Justin A. Lemkul wrote:
He, Yang wrote:
HI Justin,
I just use the mdrun command and then get such error. Before that,
I did not get other messages just go on well expect when I use the
mdrun.
Also, when I did not use the position_restraints , it will run
smoothly. As long as I add this even though the position_restraints
includes only one atom, it will show the error.
This is difficult to diagnose exactly. To me, removal of position
restraints suggests that you are fixing in place some bad contact
that is causing your system to crash. Have a look at the trajectory
to see what is going on. Did EM work properly? If you are still
having trouble, post a more complete description of your system,
relevant .mdp file(s), and anything else necessary to try to get a
resolution.
-Justin
Yang
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Tuesday, April 14, 2009 3:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the position_restraints
He, Yang wrote:
HI all users,
I want to define the position_restraints in the itp file but when
I run it, it always show that
Segmentation fault (core dumped)
You'll have to do better than "run it" - what do you mean, grompp?
mdrun?
As written, your position restraints look OK, so I don't think the
problem is
related to that section, necessarily. How have you deduced that
this is where
the problem lies?
Are you getting any other messages from (grompp? mdrun?) before the
seg fault?
-Justin
and I will list the part below:
[position_restraints]
;ai funct fc
1 1 10000 10000 10000
2 1 10000 10000 10000
3 1 10000 10000 10000
4 1 10000 10000 10000
5 1 10000 10000 10000
6 1 10000 10000 10000
7 1 10000 10000 10000
8 1 10000 10000 10000
9 1 10000 10000 10000
10 1 10000 10000 10000
11 1 10000 10000 10000
12 1 10000 10000 10000
13 1 10000 10000 10000
14 1 10000 10000 10000
15 1 10000 10000 10000
16 1 10000 10000 10000
17 1 10000 10000 10000
18 1 10000 10000 10000
19 1 10000 10000 10000
20 1 10000 10000 10000
41 1 10000 10000 10000
42 1 10000 10000 10000
43 1 10000 10000 10000
44 1 10000 10000 10000
45 1 10000 10000 10000
46 1 10000 10000 10000
47 1 10000 10000 10000
48 1 10000 10000 10000
49 1 10000 10000 10000
50 1 10000 10000 10000
51 1 10000 10000 10000
52 1 10000 10000 10000
53 1 10000 10000 10000
54 1 10000 10000 10000
55 1 10000 10000 10000
56 1 10000 10000 10000
57 1 10000 10000 10000
58 1 10000 10000 10000
59 1 10000 10000 10000
60 1 10000 10000 10000
Can anyone of you tell me what is the problem for that? Thank you
very much in advance.
Yang
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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