[gmx-users] Segmentation fault

[jahanshah ashkani]

Hi,
I have got a segmentation fault error when I run mdrun for 1ns. I would be glad if you let me know what is going on and how can I solve it.
Thank you very much.

Best,

 
Jahanshah Ashkani,
PhD student of Biotechnology & Genetics,
University of the Western Cape,
Biotechnology Department,
Private Bag X17,
7735 Bellville,
Cape Town,
South Africa
jashkani at mail.biotech.uwc.ac.za

----- Original Message ----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: JMandumpal <jesbman at rediffmail.com>
Cc: gmx-users at gromacs.org
Sent: Tuesday, December 4, 2007 4:07:36 AM
Subject: Re: Re: Re: [gmx-users] Energy minimisation


Quoting JMandumpal <jesbman at rediffmail.com>:

>
> Dear Justin,
>
> I made some changes in my .mdp file, but the result is same.
>
> My box size, as mentioned in the previous mail, is 20.1 A. The cut
 off I used
> is 8 angstrom.
>
> I attach the input file here.
> **************************************
>
> cpp            = /lib/cpp
> define         = -DPOSRES-DFLEX_SPC
> constraints    =  none
> morse          =  no
> integrator     = steep
> nsteps         = 2000
> ; Energy minimizing
> emtol          = 100
> emstep         = 0.00001
> nstcomm        = 1
> ns_type        = grid
> rlist          = 0.8
> coulumbtype    = pme
> rcoulomb       = 0.8
> vdw-type       = cut-off
> rvdw           = 0.8
> nstenergy      = 10
> Tcoupl         = no
> Pcoupl         = no
> gen_vel        = no
> *************************************************
>
> And the output message is :
>
>
 ---------------------------------------------------------------------------
> creating statusfile for 1 node...
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Excluding 2 bonded neighbours for SOL 258
> NOTE:
>   System has non-zero total charge: -2.580000e-01
>
> processing coordinates...
> double-checking input for internal consistency...
> ERROR: The cut-off length is longer than half the shortest box vector
 or
> longer than the smallest box diagonal element. Increase the box size
 or
> decrease rlist.
> -------------------------------------------------------
> Program grompp, VERSION 3.3.2
> Source code file: grompp.c, line: 1111
>
> Fatal error:
> There were 1 error(s) processing your input
> -------------------------------------------------------
>
> "Stop Drinking My Beer !" (The Amps)
>
  ----------------------------------------------------------------------
>
>
> HOW CAN I SETTLE THIS ISSUE?

Did you read Tsjerk's message from this morning?  His suggestions
 regarding PBC
and verifying your box dimensions are good ones that I had not
 considered.

Also note that you probably have a broken topology, as the net charge
 on your
system is non-integral.  This has nothing to do with the problem at
 hand, but
it will likely be problematic later.

-Justin

>
>
> REGARDS
> JESTIN
>



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

Justin A. Lemkul
Graduate Research Assistant
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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