[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

[Mohammed I Sorour]

Hi Justin,

Yes, I'm using a queuing system with a submission script.

#-l nodes=1:ppn=16

#PBS -l walltime=10:00:00

#PBS ­-qmedium

#PBS -N NVT

#PBS -e out.err

#PBS -o out



module load gromacs


cd ${PBS_O_WORKDIR}/;


gmx mdrun -deffnm nvt


Well, based on your hint, I executed a trial mdrun job without using the
queue. It seems to be working well and reading the .tpr file, I had to kill
the job once I made sure that it is reading the tpr file due to the
regulations of using the cluster out of the queue.
So, I should suspect that there is something wrong with executing the
script. It is worthy to note that I used the same script without any kind
of change multiple times and it's working well. This's more confusing for
me now, any hints?

Thanks for the ionization/neutralization advice; surely I did that.

Thanks,
Mohammed

On Thu, Aug 1, 2019 at 9:22 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/1/19 7:04 PM, Mohammed I Sorour wrote:
> >> Hi,
> >
> > that's what the ls -l prints,
> >
> >
> >
> >
> >> ls -l
> >> total 193120
> >> drwxr-xr-x 2 tuf73544 chem     4096 Jul 26 17:20 amber99sb_dyes.ff
> >> -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:56 em.gro
> >> -rw-r--r-- 1 tuf73544 chem      191 Aug  1 15:04
> equilibration_NVT_script
> >> -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:11 full_solv_ions.gro
> >> -rw-r--r-- 1 tuf73544 chem     2164 Jul  8  2016 ions.itp
> >> -rw-r--r-- 1 tuf73544 chem 33866956 Jul 31 19:08 ions.tpr
> >> -rw-r--r-- 1 tuf73544 chem    11962 Aug  1 14:57 mdout.mdp
> >> -rw-r--r-- 1 tuf73544 chem    11962 Aug  1 14:56 #mdout.mdp.1#
> >> -rw-r--r-- 1 tuf73544 chem     1875 Jul 27 08:22 nvt.mdp
> >> -rw-r--r-- 1 tuf73544 chem 39455312 Aug  1 14:57 nvt.tpr
> >> -rw------- 1 tuf73544 chem     1032 Aug  1 15:04 out
> >> -rw------- 1 tuf73544 chem     2395 Aug  1 15:04 out.err
> >> -rw-r--r-- 1 tuf73544 chem    38899 Jul 31 18:58 posre_DNA_chain_A.itp
> >> -rw-r--r-- 1 tuf73544 chem    39953 Jul 31 18:58 posre_DNA_chain_B.itp
> >> -rw-r--r-- 1 tuf73544 chem     3215 Aug  1 14:57 residuetypes.dat
> >> -rw-r--r-- 1 tuf73544 chem     4873 Jul 18 13:03 specbond.dat
> >> -rw-r--r-- 1 tuf73544 chem    69176 Jul 16 11:40 tip3p.gro
> >> -rw-r--r-- 1 tuf73544 chem   588482 Jul 31 18:58 topol_DNA_chain_A.itp
> >> -rw-r--r-- 1 tuf73544 chem   589283 Jul 31 18:58 topol_DNA_chain_B.itp
> >> -rw------- 1 tuf73544 chem     1264 Jul 31 19:10 topol.top
> >> drwxr-xr-x 3 tuf73544 chem     4096 Aug  1 14:18 trial
>
> Are you executing mdrun interactively, or via some kind of queuing
> system with a submission script?
>
> Also you should *not* be running dynamics on a system with such a net
> charge. Add salt and neutralize! It's not the source of your problem,
> though.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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