MD simulations template

This is a template/example of a pipeline for MD simulations in Gromacs and their basic analysis; in the case we use gromacs/2020.3-mpi-gpu

gmx_template guide

gmx_template is a veratile pipeline to setup and perform MD simulations using Gromacs. Below is the description of pipeline steps and files.

1 step - 100 ns MD (for tails condencation)

1_1_prepare_gmx_system_amber_tip3p.ipynb (use one of three (tip3p, opc, tip4pd) options available, required) - start with initial nucleosome strucutre with stright tails; the system of gromacs files are created here (in GMX_system_prep folder)
1_2_restraints.ipynb (optional) -in the case if we want to restrict melting of terminal DNA base pairs
2_min_equil.ipynb (required) - energy minimization and 5-step equilibration and 100 ns MD run (GMX_run_prep folder)

Note! The result of the step is in the GMX_system_prep/sys_condensed.pdb file

2 step - 2 us MD

3_1_prepare_gmx_system_amber_tip3p.ipynb (required) -the same as 1st step but for condenced system; use appropriate water model prefix
3_2_min_equil.ipynb (required) - energy minimization and equilibration step
4_1_production_tpr.ipynb (required) - preparation of tpr file(s) for MD
4_2_production_start_run.ipynb (required) - MD simulation run (on Lomonosov supercomputer)
5_trj_preprocessing.ipynb (required) - trajectory preprocessing
6_0_quality_control.ipynb - analysis of temperature, presure etc, periodic images

config.py - modify config.py ssh_host - host in .ssh/configure that will be used to connect to a remote machine run_profile - host-dependent profile