[gmx-users] the position_restraints

[XAvier Periole]

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-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
>> ========================================
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
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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
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
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