Output files:

This repository contains the files of simulations for the timestep choice manuscript (current version available at https://doi.org/10.26434/chemrxiv-2025-jwkz1)

Test run Example

To run the simulation using the provided script, download the necessary files from the links below:

Topology file: ti_hmr_L00.parm7
Initial coordinate file: 0.00000000_npt_0.0005.rst7
Input files: inputs/

Batch Script for NVE Simulations using AMBER

This Bash script sample_hmr_on_shake_on_step_3_nve.sh Link automates the setup and submission of molecular dynamics simulations under NVE ensembles across different time steps and lambda windows using AMBER on an HPC cluster.

Automated NVE Simulation Submission Script (Single Lambda)

This script is designed to automate the setup and submission of 100 ns NVE simulations for a single lambda value using AMBER with CUDA acceleration on a SLURM-based HPC cluster.

System Setup

Lambda value: 0.00000000
Topology file: ti_hmr_L00.parm7
Starting restart file for all NVE simulations: 0.00000000_npt_0.0005.rst7

Time Step Configurations

Time Step (ps)	NVE Total Steps	Output Frequency
0.0005	200,000,000	2000
0.001	100,000,000	1000
0.002	50,000,000	500
0.0025	40,000,000	400
0.00333333	30,000,000	300
0.004	25,000,000	250

Files and Structure

Input folder: inputs/ — auto-generated NVE .mdin files
Run folder: run/ — simulation outputs
Job scripts: job_{lambda}_{dt}.sh — one per timestep

Each .mdin file is uniquely created per timestep, with key MD parameters for NVE runs.

SLURM Job Script Sample

#!/bin/bash
#SBATCH --job-name=aq_0.00000000_0.001
#SBATCH --partition=gpu
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --gres=gpu:1
#SBATCH --mem=32G
#SBATCH --time=3-00:00:00
#SBATCH --error=job_0.00000000_0.001.err
#SBATCH --output=job_0.00000000_0.001.out
#SBATCH [email protected]
#SBATCH --nodelist=gpu[019-020,022-026]

# Load necessary modules
module purge
module use /projects/community/modulefiles
module load gcc/10.2.0/openmpi/4.0.5-bz186
module load cmake/3.19.5-bz186
module load cuda/11.7.1

# Load AMBER
source /home/sp2546/softwares/AMBER/amber24/amber.sh

# Run NVE simulation
pmemd.cuda -O \
  -p ti_hmr_L00.parm7 \
  -c inicord/0.00000000_npt_0.0005.rst7 \
  -i inputs/0.00000000_nve_0.001.mdin \
  -o run/0.00000000_nve_0.001.mdout \
  -r run/0.00000000_nve_0.001.rst7 \
  -x run/0.00000000_nve_0.001.nc \
  -inf run/0.00000000_nve_0.001.mdinfo \
  -AllowSmallBox

After executing the sample_hmr_on_shake_on_step_3_nve.sh script, the following output files will be generated by the AMBER package for each simulation:

.mdout — standard output log of the simulation
.nc — trajectory file in NetCDF format
.rst7 — final restart coordinate file
.mdinfo — performance and energy statistics These files will be saved in the specified run/ directory.

Analysis

To analyze the simulation results, follow these steps:

Create a folder named results
```
mkdir results
```
Download the analysis scripts:
- step_1_extract_1.py
- step_8_extract.py
Download and execute the analysis runner script:
- run_analysis.sh

The script will automate post-processing and data extraction using the provided Python tools. Make sure Python and any required libraries are installed in your environment before running the analysis.

Directory: DATA

subdirectory: c-md

Camp System

Path: DATA/c-md/camp

hmr_off_shake_off
Link
- Topology: ti_L00.parm7
  (Located at DATA/c-md/camp/hmr_off_shake_on)
- Initial coordinate: 0.00000000_npt_0.0005.rst7
  (Located at DATA/c-md/camp/hmr_off_shake_on/inicord)
- mdin: (Located at DATA/c-md/camp/hmr_off_shake_off/inputs)
hmr_off_shake_on
Link
- Topology: ti_L00.parm7
  (Located at DATA/c-md/camp/hmr_off_shake_on)
- Initial coordinate: 0.00000000_npt_0.0005.rst7
  (Located at DATA/c-md/camp/hmr_off_shake_on/inicord)
- mdin: (Located at DATA/c-md/camp/hmr_off_shake_on/inputs)
hmr_on_shake_off
Link
- Topology: ti_hmr_L00.parm7
  (Located at DATA/c-md/camp/hmr_on_shake_off)
- Initial coordinate: out_L00.rst7
  (Located at DATA/c-md/camp/hmr_on_shake_off/inicord)
- mdin: (Located at DATA/c-md/camp/hmr_on_shake_off/inputs)
hmr_on_shake_on
Link
- Topology: ti_hmr_L00.parm7
  (Located at DATA/c-md/camp/hmr_on_shake_on)
- Initial coordinate: out_L00.rst7
  (Located at DATA/c-md/camp/hmr_on_shake_on/inicord)
- mdin: (Located at DATA/c-md/camp/hmr_on_shake_on/inputs)

Ethane System

Path: DATA/c-md/ethane

hmr_off_shake_off
Link
- Topology: out_L00.parm7
  (Located at DATA/c-md/ethane/hmr_off_shake_on)
- Initial coordinate: 0.00000000_npt_0.0005.rst7
  (Located at DATA/c-md/ethane/hmr_off_shake_on/inicord)
- mdin: (Located at DATA/c-md/ethane/hmr_off_shake_off/inputs)
hmr_off_shake_on
Link
- Topology: out_L00.parm7
  (Located at DATA/c-md/ethane/hmr_off_shake_on)
- Initial coordinate: 0.00000000_npt_0.0005.rst7
  (Located at DATA/c-md/ethane/hmr_off_shake_on/inicord)
- mdin: (Located at DATA/c-md/ethane/hmr_off_shake_on/inputs)
hmr_on_shake_off
Link
- Topology: out_hmr_L00.parm7
  (Located at DATA/c-md/camp/hmr_on_shake_off)
- Initial coordinate: out_L00.rst7
  (Located at DATA/c-md/ethane/hmr_on_shake_off/inicord)
- mdin: (Located at DATA/c-md/ethane/hmr_on_shake_off/inputs)
hmr_on_shake_on
Link
- Topology: out_hmr_L00.parm7
  (Located at DATA/c-md//hmr_on_shake_on)
- Initial coordinate: out_L00.rst7
  (Located at DATA/c-md/ethane/hmr_on_shake_on/inicord)
- mdin: (Located at DATA/c-md/ethane/hmr_on_shake_on/inputs)

subdirectory ti-md

camp to rp-camp transformation

Path: DATA/ti-md/camp_rpcamp

hmr_on_shake_on_all_sc
Link
- Topology: ti_hmr.parm7
  (Located at DATA/ti-md/camp_rpcamp/hmr_on_shake_on_all_sc)
- Initial coordinate: 0.00000000_npt_0.0005.rst7
  (Located at DATA/ti-md/camp_rpcamp/hmr_on_shake_on_all_sc/inicord)
- mdin: (Located at DATA/ti-md/camp_rpcamp/hmr_on_shake_on_all_sc/inputs)
hmr_on_shake_on_no_sc
Link
- Topology: ti_hmr.parm7
  (Located at DATA/ti-md/camp_rpcamp/hmr_on_shake_on_no_sc)
- Initial coordinate: 0.00000000_npt_0.0005.rst7
  (Located at DATA/ti-md/camp_rpcamp/hmr_on_shake_on_no_sc/inicord)
- mdin: (Located at DATA/ti-md/camp_rpcamp/hmr_on_shake_on_no_sc/inputs)
hmr_on_shake_on_one_sc
Link
- Topology: ti_hmr.parm7
  (Located at DATA/ti-md/camp_rpcamp/hmr_on_shake_on_one_sc)
- Initial coordinate: 0.00000000_npt_0.0005.rst7
  (Located at DATA/ti-md/camp_rpcamp/hmr_on_shake_on_one_sc/inicord)
- mdin: (Located at DATA/ti-md/camp_rpcamp/hmr_on_shake_on_one_sc/inputs)

ethane to ethanol transformation

Path: DATA/ti-md/ethane_ethanol/

hmr_on_shake_on_3_atom_sc
Link
- Topology: out_hmr.parm7
  (Located at DATA/ti-md/ti-md/ethane_ethanol/hmr_on_shake_on_3_atom_sc)
- Initial coordinate: 0.00000000_npt_0.0005.rst7
  (Located at DATA/ti-md/ti-md/ethane_ethanol/hmr_on_shake_on_3_atom_sc/inicord)
- mdin: (Located at DATA/ti-md/ti-md/ethane_ethanol/hmr_on_shake_on_3_atom_sc/inputs)
hmr_on_shake_on_all_sc
Link
- Topology: out_hmr.parm7
  (Located at DATA/ti-md/ti-md/ethane_ethanol/hmr_on_shake_on_all_sc)
- Initial coordinate: 0.00000000_npt_0.0005.rst7
  (Located at DATA/ti-md/ti-md/ethane_ethanol/hmr_on_shake_on_all_sc/inicord)
- mdin: (Located at DATA/ti-md/ti-md/ethane_ethanol/hmr_on_shake_on_all_sc/inputs)

Subdirectory: `ti_t_test`

This directory contains input files for Thermodynamic Integration (TI) simulations to evaluate statistical consistency using a t-test. Each simulation runs for 10 ns and is repeated 8 times for robust statistical analysis.

Path: DATA/ti_t_test/

ejm 42 to ejm 55 transformation

Repository Link: git_hub_ejm_42~ejm_55

Environment: `aq`

Path: aq
Topology File: unisc.parm7
(Located at DATA/ti_t_test/git_hub_ejm_42~ejm_55/aq)

lambda=0 (Located at DATA/ti_t_test/git_hub_ejm_42~ejm_55/aq/lambda0)

lambda=0.25 (Located at DATA/ti_t_test/git_hub_ejm_42~ejm_55/aq/lambda025)

lambda=0.5 (Located at DATA/ti_t_test/git_hub_ejm_42~ejm_55/aq/lambda05)

lambda=0.75 (Located at DATA/ti_t_test/git_hub_ejm_42~ejm_55/aq/lambda075)

lambda=1.00 (Located at DATA/ti_t_test/git_hub_ejm_42~ejm_55/aq/lambda1)

Environment: `com`

Path: com
Topology File: unisc.parm7
(Located at DATA/ti_t_test/git_hub_ejm_42~ejm_55/com)

lambda=0 (Located at DATA/ti_t_test/git_hub_ejm_42~ejm_55/com/lambda0)

lambda=0.25 (Located at DATA/ti_t_test/git_hub_ejm_42~ejm_55/com/lambda025)

lambda=0.5 (Located at DATA/ti_t_test/git_hub_ejm_42~ejm_55/aq/lambda05)

lambda=0.75 (Located at DATA/ti_t_test/git_hub_ejm_42~ejm_55/com/lambda075)

lambda=1.00 (Located at DATA/ti_t_test/git_hub_ejm_42~ejm_55/com/lambda1)

ethane to ethanol transformation

Repository Link: git_hub_ethane_ethanol

all SC

lambda=0 (Located at DATA/ti_t_test/git_hub_ethane_ethanol/SCAll_lambda0)

lambda=0.25 (Located at DATA/ti_t_test/git_hub_ethane_ethanol/SCAll_lambda025)

lambda=0.5 (Located at DATA/ti_t_test/git_hub_ethane_ethanol/SCAll_lambda05)

lambda=0.75 (Located at DATA/ti_t_test/git_hub_ethane_ethanol/SCAll_lambda075)

lambda=1.00 (Located at DATA/ti_t_test/git_hub_ethane_ethanol/SCAll_lambda1)

4/5-atom SC

lambda=0 (Located at DATA/ti_t_test/git_hub_ethane_ethanol/lambda0)

lambda=0.25 (Located at DATA/ti_t_test/git_hub_ethane_ethanol/lambda025)

lambda=0.5 (Located at DATA/ti_t_test/git_hub_ethane_ethanol/lambda05)

lambda=0.75 (Located at DATA/ti_t_test/git_hub_ethane_ethanol/lambda075)

lambda=1.00 (Located at DATA/ti_t_test/git_hub_ethane_ethanol/lambda1)

camp to rp-camp transformation

Repository Link: git_hub_CampTI

no SC

lambda=0 (Located at DATA/ti_t_test/git_hub_CampTI/NoSC_lambda_0)

lambda=0.25 (Located at DATA/ti_t_test/git_hub_CampTI/NoSC_lambda_25)

lambda=0.5 (Located at DATA/ti_t_test/git_hub_CampTI/NoSC_lambda_05)

lambda=0.75 (Located at DATA/ti_t_test/git_hub_CampTI/NoSC_lambda_75)

lambda=1.00 (Located at DATA/ti_t_test/git_hub_CampTI/NoSC_lambda_1)

1 atom

lambda=0 (Located at DATA/ti_t_test/git_hub_CampTI/SC_lambda_0)

lambda=0.25 (Located at DATA/ti_t_test/git_hub_CampTI/SC_lambda_25)

lambda=0.50 (Located at DATA/ti_t_test/git_hub_CampTI/SC_lambda_05)

lambda=0.75 (Located at DATA/ti_t_test/git_hub_CampTI/SC_lambda_75)

lambda=1.00 (Located at DATA/ti_t_test/git_hub_CampTI/SC_lambda_1)

all SC

lambda=0 (Located at DATA/ti_t_test/git_hub_CampTI/SCAll_lambda_0)

lambda=0.25 (Located at DATA/ti_t_test/git_hub_CampTI/SCAll_lambda_25)

lambda=0.50 (Located at DATA/ti_t_test/git_hub_CampTI/SCAll_lambda_05)

lambda=0.75 (Located at DATA/ti_t_test/git_hub_CampTI/SCAll_lambda_75)

lambda=1.00 (Located at DATA/ti_t_test/git_hub_CampTI/SCAll_lambda_1)

Output files:

Due to the file sizes, all input and output files are available through anonymous ftp to 165.230.21.2.

Name		Name	Last commit message	Last commit date
Latest commit History 194 Commits
DATA		DATA
analysis_code		analysis_code
README.md		README.md

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Test run Example

Batch Script for NVE Simulations using AMBER

Automated NVE Simulation Submission Script (Single Lambda)

System Setup

Time Step Configurations

Files and Structure

SLURM Job Script Sample

Analysis

Directory: DATA

subdirectory: c-md

Camp System

Ethane System

subdirectory ti-md

camp to rp-camp transformation

ethane to ethanol transformation

Subdirectory: `ti_t_test`

ejm 42 to ejm 55 transformation

Environment: `aq`

Environment: `com`

ethane to ethanol transformation

camp to rp-camp transformation

Output files:

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Test run Example

Batch Script for NVE Simulations using AMBER

Automated NVE Simulation Submission Script (Single Lambda)

System Setup

Time Step Configurations

Files and Structure

SLURM Job Script Sample

Analysis

Directory: DATA

subdirectory: c-md

Camp System

Ethane System

subdirectory ti-md

camp to rp-camp transformation

ethane to ethanol transformation

Subdirectory: ti_t_test

ejm 42 to ejm 55 transformation

Environment: aq

Environment: com

ethane to ethanol transformation

camp to rp-camp transformation

Output files:

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Subdirectory: `ti_t_test`

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