[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

[John Whittaker]

> 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?

What is the output from the cluster? I'm guessing the output is in the
file called "out" that's created each time the simulation fails.


>
> 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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