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MultiGRO

Bash shell scripts for GROMACS to run multiple simulations and their analysis at once.

MultiGRO

MultiGRO consists of two seperated components;

  1. 21 step equilibration: It is well known 21 step decompression equilibration method.
  2. PVT Curves for Tg values: A method to create PVT curves for glass transition temperature (Tg).

Still in WIP STAGE Transition from bash to python is ongoing, the expected final package will be finished within three months

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Dependencies

  • GROMACS 2021 with MPI is needed to be installed. The scripts needs to be modified for older versions since -r argument has been added for grompp module in 2021 version.

     # Add gromacs 'gmx_mpi' path:
 export PATH='*path_to_gromacs*/bin/':$PATH

Usage

21 Step Equilibration

21 step equilibration is a well known method that is used for equilibration at the initial state of amorphous. 21step.sh is located at 21step/ directory and starts a loop run which uses 21step/inputs/*.mdp files as inputs.

  • Run structure:
./21step.sh -n number_cores -c initial.gro

-n: number of cores (integer)
-c: initial .gro structure file
* Script needs topology (.top) and index file (.ndx) in the same folder.

PVT Curves

Pressure-volume-temperature (PVT) curves are used to determine glass transition temperature (Tg) of materials. run_tg.sh is located at pvt_curves/ directory and starts a loop run from the specified starting temperature to specified ending temperature with an inverval of 25 K.

  • Run structure:
./run_tg.sh -n number_cores -f user.mdp -c initial.gro -i starting_temp -m ending_temp

-n: number of cores (integer)
-f: GROMACS .mdp inputfile
-c: initial .gro structure file
-i: Starting temperature of PVT (integer, kelvin)
-m: Ending Temperature of PVT (integer, kelvin)
* Script needs topology (.top) and index file (.ndx) in the same folder.

  • As an example, if simulation would be run from 700K to 150K with user.mdp and initial.gro using 12 cores:
chmod a+x run_tg.sh
./run_tg.sh -n 12 -f user.mdp -c initial.gro -i 700 -m 150
  • Densities can be extracted using denity.sh, which is located at pvt_curves/analysis/:
chmod a+x density.sh
./density.sh i starting_temp -m ending_temp -d density_code -b starting_step
#example for run above
./density.sh -i 700 -m 150 -d 20 -b 4500
* Output includes three columns; density, standard error and rmsd.