Hi everyone, I have found out that positions restrains is the issue in my FEP simulation. As soon as I switch off position restraints it works fine. I have the following the restraint file for the ions in my system (I don't see any problems with it):
*[ position_restraints ]; atom type fx fy fz 1 1 0 0 1000 2 1 0 0 1000 3 1 0 0 1000 4 1 0 0 1000 5 1 0 0 1000 6 1 0 0 1000 8 1 0 0 1000 9 1 0 0 1000 10 1 0 0 1000 11 1 0 0 1000 12 1 0 0 1000 13 1 0 0 1000 14 1 0 0 1000 15 1 0 0 1000 16 1 0 0 1000 17 1 0 0 1000 18 1 0 0 1000 19 1 0 0 1000 20 1 0 0 1000 21 1 1000 1000 1000;[ position_restraints ] ; flat bottom position restraints, here for potassium in site I; type, g(8 for a cylinder), r(nm), k 7 2 8 1 1000* On 22 August 2017 at 14:18, Vikas Dubey <vikasdubey...@gmail.com> wrote: > Hi, I use the following script for my cluster. Also, I think problem is > calculation specific. I have run a quite a few normal simulations , it > works fine : > > > #SBATCH --job-name=2_1_0 > #SBATCH --mail-type=ALL > #SBATCH --time=24:00:00 > #SBATCH --nodes=1 > #SBATCH --ntasks-per-node=1 > #SBATCH --ntasks-per-core=2 > #SBATCH --cpus-per-task=4 > #SBATCH --constraint=gpu > #SBATCH --output out.txt > #SBATCH --error err.txt > #======================================== > # load modules and run simulation > module load daint-gpu > module load GROMACS > export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK > export CRAY_CUDA_MPS=1 > > srun -n $SLURM_NTASKS --ntasks-per-node=$SLURM_NTASKS_PER_NODE -c > $SLURM_CPUS_PER_TASK gmx_mpi mdrun -deffnm md_0 > > On 22 August 2017 at 06:11, Nikhil Maroli <scinik...@gmail.com> wrote: > >> Okay, you might need to consider >> >> gmx mdrun -v -ntmpi XX -ntomp XX -deffnm XXXX -gpu_id XXX >> >> >> >> http://manual.gromacs.org/documentation/5.1/user-guide/mdrun >> -performance.html >> >> http://www.gromacs.org/Documentation/Errors#There_is_no_ >> domain_decomposition_for_n_nodes_that_is_compatible_with_the >> _given_box_and_a_minimum_cell_size_of_x_nm >> -- >> 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.