[gmx-users] the position_restraints

[He, Yang]

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.

Yang
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at 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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