Hi, Does it work if you just have the normal position restraints, or just have the flat-bottom restraints? In particular, I could image the latter are not widely used and might have a bug.
Mark On Thu, Aug 24, 2017 at 4:36 PM Vikas Dubey <[email protected]> wrote: > 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 <[email protected]> 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 <[email protected]> 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 [email protected]. > >> > > > > > -- > 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 [email protected]. > -- 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 [email protected].
