[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

[Justin Lemkul]

On 8/2/19 10:49 AM, Mohammed I Sorour wrote:
> 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}/;

Can you verify that this command is putting you in the directory you 
think? The environment variable points to the directory from which the 
job was submitted, so if your submission script and input files are not 
in the same directory, you're telling the queue to move into 
$PBS_O_WORKDIR, where it fails to find nvt.tpr

-Justin

>
> 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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-- 
==================================================

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

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