MultiGRO

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

MultiGRO consists of two seperated components;

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

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 (T_g) 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.