[gmx-users] FEP calculations on multiple nodes
Vikas Dubey
vikasdubey055 at gmail.com
Thu Aug 24 16:36:39 CEST 2017
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 <vikasdubey055 at 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 <scinikhil at 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
>> --
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