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

Mark Abraham mark.abraham at anu.edu.au
Mon Jun 15 08:38:45 CEST 2009

On 06/15/09, Bhanu  <bhanuiitr at gmail.com> wrote:
> 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.

>  For this experiment, here is the error report which I donot understand at all!
> The error report is really frightening to me!!! Here it is!

See http://oldwiki.gromacs.org/index.php/Errors#Range_Checking_error


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