[gmx-users] the position_restraints

[Justin A. Lemkul]

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
> 
> ========================================
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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

========================================