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 <jalem...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.