Desmond

Desmond is D. E. Shaw Research’s GPU molecular-dynamics engine. Academic and not-for-profit use is free of charge; the cluster install uses that academic license.

Desmond is GPU-oriented. Request a GPU (Job submission).

This module is the Desmond academic bundle, not the full Schrödinger Suite (mm/schrodinger). Do not load both at once: both set $SCHRODINGER.

Load

$ module load md/desmond

Example

Prepare the system in Maestro (on a workstation with a display) or with $SCHRODINGER/run. Submit the MD on the cluster:

#!/bin/bash
#SBATCH -J desmond
#SBATCH -c 8
#SBATCH --mem-per-cpu=4G
#SBATCH --gpus=2080ti:1
#SBATCH -t 24:00:00
#SBATCH -o %x-%j.out

module load md/desmond
WORKDIR="$SCRATCH_DIR/$SLURM_JOB_ID"
mkdir -p "$WORKDIR"
cd "$WORKDIR"
cp "$SLURM_SUBMIT_DIR"/*.cms "$SLURM_SUBMIT_DIR"/*.cfg . 2>/dev/null || true

srun $SCHRODINGER/desmond -WAIT -in job.cfg

Adjust -in to your Desmond config name. Copy keepers back to $DATA_DIR or the submit directory when the job finishes.

Maestro’s GUI needs a local display; it is not meant for the login node or a headless compute node.