CALVADOS

The CALVADOS package is used for performing simulations of biomolecules using OpenMM and the coarse-grained CALVADOS model. The package makes it easy to run simulations using the family of CALVADOS models of biomolecules including disordered proteins, multi-domain proteins, proteins in crowded environments, and disordered RNA. Link to the description.

Availability

Cluster	Module/Version
BOSE	calvados/0.8.0
BGSC	None

Note: You can simply use module load calvados to activate the most recently installed version of this software.

Commands

Below is a list of importable modules.

Importable Modules
analysis
build
cfg
components
interactions
sequence
sim
utilities

CALVADOS Examples

The install files for CALVADOS include several examples you can use. Before you run them, it's recommended to copy the examples to your own folder first.

module load calvados/0.8.0
cp -r $CALVADOS_DIR/examples ./calvados_examples

GPU-Based Job

Several example scripts can take advantage of GPU-acceleration for significant boost in performance. If available, their documentation may mention an argument such as --gpu_id, which you can set to $CUDA_VISIBLE_DEVICES. Note that your job must be set to use a GPU card for this to be effective.

python script.py --gpu_id=$CUDA_VISIBLE_DEVICES

Sample Slurm Script

This example Slurm script is based off an example provided by CALVADOS.

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load calvados/0.8.0    # Load CALVADOS

cp -r $CALVADOS_DIR/examples ./calvados_examples
cd calvados_examples/single_IDR
python prepare.py --name FUSRGG3
python FUSRGG3/run.py --path FUSRGG3

Real Example

Has your research group used CALVADOS in a project? Contact the HPC Team and we'd be glad to feature your work.

Citations

Please include the following citation in your papers to support continued development of CALVADOS.

G. Tesei, T. K. Schulze, R. Crehuet, K. Lindorff-Larsen. Accurate model of liquid-liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties. PNAS (2021), 118(44):e2111696118. DOI: 10.1073/pnas.2111696118

G. Tesei, K. Lindorff-Larsen. Improved predictions of phase behaviour of intrinsically disordered proteins by tuning the interaction range. Open Research Europe (2022), 2(94). DOI: 10.12688/openreseurope.14967.2

F. Cao, S. von Bülow, G. Tesei, K. Lindorff-Larsen. A coarse-grained model for disordered and multi-domain proteins. Protein Science (2024), 33(11):e5172. DOI: 10.1002/pro.5172