GrandFEP CLI

run_GC_RE.py

Run GrandFEP REST2+GCMC simulations

Example

for win in {0..15}
do
    mkdir $win/0 $win/1
done
mpirun -np 16 $script_dir/run_GC_RE.py \
    -pdb    system.pdb \
    -system system.xml.gz \
    -multidir 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 \
    -yml gc_eq.yml \
    -maxh 18 \
    -ncycle 576 \
    -start_rst7   gc_start.rst7 \
    -start_jsonl  gc_start.jsonl \
    -deffnm       0/gc

mpirun -np 16 $script_dir/run_GC_RE.py \
    -pdb    system.pdb \
    -system system.xml.gz \
    -multidir 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 \
    -yml gc.yml \
    -maxh 9 \
    -ncycle 1200 \
    -start_rst7  0/gc.rst7 \
    -start_jsonl 0/gc.jsonl \
    -deffnm      1/gc

Description

This script combines MD / GC / RE. It requires pdb file as topology, system xml file as system definition, yaml file as simulation parameters, and multiple directories for different lambdas.

run_NPT_RE.py

Run NPT REST2+GCMC simulations

Example

for win in {0..15}
do
    mkdir $win/0 $win/1
done
mpirun -np 16 $script_dir/run_NPT_RE.py \
    -pdb    system.pdb \
    -system system.xml.gz \
    -multidir 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15  \
    -yml npt.yml \
    -maxh 10 \
    -ncycle 1000 \
    -start_rst7  npt_eq.rst7 \
    -deffnm      0/npt
mpirun -np 16 $script_dir/run_NPT_RE.py \
    -pdb    system.pdb \
    -system system.xml.gz \
    -multidir 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15  \
    -yml npt.yml \
    -maxh 10 \
    -ncycle 1000 \
    -start_rst7  0/npt.rst7 \
    -deffnm      1/npt