[gmx-users] Strange error in DNA simulations..

[Mark Abraham]

On 06/15/09, Bhanu  <bhanuiitr at gmail.com> wrote:
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> On 15/06/2009, Mark Abraham <mark.abraham at anu.edu.au <mark.abraham at anu.edu.au>> wrote:
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> > On 06/15/09, Bhanu <bhanuiitr at gmail.com <bhanuiitr at gmail.com>> wrote: 
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> > > 
> > > Hi Group,
> > > I've tried simulating a five bp dna. It has showed many atoms missing and some extra atoms present in the pdb file. For pdb2gmx, I used -ignh and -mising options. Later editconf_d, genbox_d, and genion_d steps went well. Even grompp_d worked well. But when I issued the run command for mdrun_d, the strange result is coming, repeatedly. I have installed lam-mpi and running gromacs in double precision. The commands I have used are..
> > > 
> > > pdb2gmx_d -f fivedna.pdb -o dna.gro -p dna.top 
> > > editconf_d -f dna.gro -bt dodecahedron -c -d 1.0 -o boxdna.gro
> > > genbox_d -cp boxdna.gro -cs spc216.gro -p dna.top -o solvateddna.gro
> > > 
> > > neutralized the system with genion_d and grompp_d, mdrun_d with -v and -deffnm commands. Surprisigly, everytime, it is using only two cores of my core2quad processor, delaying the output for all experiments.
> > So look up how to configure LAM-MPI to use more.
> 
>  
> I am working on that.. but the real confusing thing, is why are DNA simulations failing?? I have no clue.. and requesting for a suggestion!
I gave you a link to content that was likely to explain why your problem was occurring. If you appear to ignore it, then you won't be likely to get more :-)

Mark

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> > > For this experiment, here is the error report which I donot understand at all!
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> > > The error report is really frightening to me!!! Here it is!
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> > See http://oldwiki.gromacs.org/index.php/Errors#Range_Checking_error (http://oldwiki.gromacs.org/index.php/Errors#Range_Checking_error)
> > 
> > Mark
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> -- 
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