Mesoscopic Multiscale Simulations

Description

Simplified Use Case for the OpenModel project. This workflow aims to create a sample of 512 water molecules (TIP4P 2005 model). The workflow starts with a coarse-grained force field based on the MOLC model, implemented in a fork of LAMMPS, version 2_Jun 2022. The sample is first assembled in the desired configuration, annealed, converted to atomistic coordinates with the program BACKMAP, and finally annealed with a type-I atomistic force field (OPLS).

The whole procedure is based on open-source software and relies on a coarse-grained force field parametrised consistently with the atomistic force field. Since LAMMPS has limited capabilities to handle complex structures, the strategy used here is to manipulate molecular samples with a custom-written program, dumptools, and to combine the structure with the force field using MOLTEMPLATE.

Software Dependency

This Use Case depends on the following software. Additional scripts are included in the scripts folder.

1. MOLTEMPLATE.
2. LAMMPS_MOLC, patch June 2022, including the USER-MOLC package.
3. BACKMAP.
4. VMD.

Workflow

Go to the multiscale folder and execute the following steps.

1. Create a cubic box of coarse-grained TIP4P-2005 water molecules. Anneal and equilibrate the structure with LAMMPS.

   bash 01_step.sh

2. Post-process the output:

• Wrap the last frame of the CG trajectory.
• Convert the CG snapshot to atomic coordinates.
• Render the backmapped structure and the force field with MOLTEMPLATE.
• Run the atomistic MD simulation with LAMMPS.

  bash 02_step.sh

3. EXTRA: create a PSF topology file to visualize the binary trajectory:

   data2psf 02_water_aa.data 02_water_bm.pdb
   vmd -psf 02_water_aa.psf -dcd 02_water_aa.dcd

Notes

LAMMPS 2Jun22 has been compiled with the following packages enabled:

make yes-asphere yes-kspace yes-mc yes-misc yes-molecule yes-rigid yes-asphere yes-molc yes-extra-dump yes-class2
make -j4 g++_openmpi

Agile Software Development

The first simulation to validate the verification & validation services is located in the agile01 folder. Its scope is limited to computing the density of a small box of water. The input variables of the LAMMPS template (.LT) script are commented and correspond to the metadata for this task.

The simulation depends on MOLTEMPLATE and will run on any version of LAMMPS.