NAMD [IT-Bereich des Instituts für Chemie]

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====== NAMD ======

<code bash namdjob>
#!/bin/bash --login

###################################################################################################
# WARNING: Please adapt all relevant parameters so that they fit the requirements of your job(s).                                                                                             #
###################################################################################################

# #SBATCH -o %x.%j.%N.out  # for debugging purposes: redirect SLURM's stdout (please see man 1 sbatch for explanation of replacement symbols)
# #SBATCH -e %x.%j.%N.err  # for debugging purposes: redirect SLURM's stderr (please see man 1 sbatch for explanation of replacement symbols)
# #SBATCH --mail-type=END       # if your want to receive notifications about job status (cf. man 1 sbatch)
# #SBATCH --mail-user=username

#SBATCH -J NAMDJOB              # job name/description
#SBATCH -c 4                   # total number of tasks/cores for your job
#SBATCH --hint=nomultithread     # IMPORTANT: hyper-threading is activated; switch off and attribute whole core to task
#SBATCH -N 1                    # number of nodes
#SBATCH -p gpu                # partition the job gets scheduled: standard (default), smp, gpu (uncomment, if you want your job to run on hosts in SMP partition)
#SBATCH --gres=gpu:1     # demand GPU resources (please do not use more than 1 CUDA accelerator per NAMD job; NAMD does not benefit from several accelerators and you will waste precious computing resources!)
#SBATCH --time=00:15:00         # job run (wall clock) time in HH:MM:SS
#SBATCH --mem=4GB               # amount of resident main memory PER NODE(!)
# #SBATCH --mail-type=END
# #SBATCH --mail-user=username


# loading NAMD module
module use /home/units/Fak_II/chemie/modules
module add biomodeling/namd/2.13


# Launching NAMD (please do not employ option switches +devices and+p !)
# namd2 [name_of_input_file]

</code>

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date of revision: 02-26-2020 © kraus
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