Script

Tutorial

Here is an example of a short simulation of the SH3 domain of phospholipase Cγ1. Seven successive steps are used:

Topologie creation using create_top.py.
Minimisation of the structure using minimize_pdb.py.
Solvation of the system using solvate_ions.py.
Minimisation of the system using minimize_pdb.py.
Equilibration of the system using equi_3_step.py.
Production run using production.py.
Extension of the production run using extend.py.

# Create topologie
create_top.py -f gromacs_py/test_files/1y0m.pdb -o tmp/1y0m/top -vsite

# Minimize the protein structure
minimize_pdb.py -f tmp/1y0m/top/1y0m_pdb2gmx_box.pdb -p tmp/1y0m/top/1y0m_pdb2gmx.top -o tmp/1y0m/em/  -n em_1y0m -nt 2

# Add water and ions
solvate_ions.py -f tmp/1y0m/em/em_1y0m_compact.pdb -p tmp/1y0m/top/1y0m_pdb2gmx.top -o tmp/1y0m_water_ions/top/  -n 1y0m_water_ions

# Minimize the system
minimize_pdb.py -f tmp/1y0m_water_ions/top/1y0m_water_ions_water_ion.gro -p tmp/1y0m_water_ions/top/1y0m_water_ions_water_ion.top -o tmp/1y0m_water_ions/em/  -n em_1y0m

# Do three small equilibrations with postion contraints on heavy atoms (first), Carbon alpha (second) and low constraint on Carbon alpha (third)
equi_3_step.py -f tmp/1y0m_water_ions/em/em_1y0m_compact.pdb -p tmp/1y0m_water_ions/top/1y0m_water_ions_water_ion.top -o tmp/1y0m_water_ions/  -n 1y0m -HA_time 0.1 -dt_HA 0.002 -CA_time 0.1 -CA_LOW_time 0.1 -dt 0.004 -maxwarn 1

# Small production run of 0.1 ns
production.py -f tmp/1y0m_water_ions/02_equi_CA_LOW/equi_CA_LOW_1y0m.gro -p tmp/1y0m_water_ions/top/1y0m_water_ions_water_ion.top -o tmp/1y0m_water_ions/03_prod -n 1y0m -time 0.1 -dt 0.004 -maxwarn 1

# Extension of the simulation
extend.py -s tmp/1y0m_water_ions/03_prod/prod_1y0m.tpr -time 0.2

# Remove simulation files
rm -r ./tmp

Or simply use one command to do all previous commands:

top_em_equi_3_step_prod.py -f gromacs_py/test/input/1y0m.pdb -o tmp/1y0m -vsite -HA_time 0.1 -CA_time 0.1 -CA_LOW_time 0.1 -prod_time 0.3

Simulation:

Energy minimization

Minimize a pdb structure in 2 steps,the first step without bonds constraints and the second step with

usage: minimize_pdb.py [-h] -f F -p P -o O -n NAME [-m_steps MIN_STEPS]
                       [-box BOX] [-nt NT] [-ntmpi NTMPI] [-gpu_id GPUID]

Named Arguments

-f: Input PDB file
-p: Topologie in gromacs format .top
-o: Output Directory
-n: Output file name
-m_steps: Minimisation nsteps, default=1000
-box: Create a box, default=False
-nt: Total number of threads to start, default=0
-ntmpi: Number of thread-MPI threads to start, default=0
-gpu_id: List of GPU device id-s to use, default=””

Equilibration

Equilibrate in 3 steps a system (coor+top), (i) first equilibration with heavy atoms position restraints, (ii) second equilibration with alpha carbon position restraints and (iii) finaly equilibration with weak alpha carbon position restraints

usage: equi_3_step.py [-h] -f F -p P -o O -n NAME [-HA_time HA_TIME]
                      [-CA_time CA_TIME] [-CA_LOW_time CA_LOW_TIME]
                      [-dt_HA DT_HA] [-dt DT] [-maxwarn MAXWARN] [-nt NT]
                      [-ntmpi NTMPI] [-gpu_id GPUID]

Named Arguments

-f: Input PDB file
-p: Topologie in gromacs format .top
-o: Output Directory
-n: Output file name
-HA_time: Equilibration with HA constraint time(ns), default = 0.25ns
-CA_time: Equilibration with HA constraint time(ns), default = 1ns
-CA_LOW_time: Equilibration with HA constraint time(ns), default = 5ns
-dt_HA: Equi HA dt, default=0.002 (2 fs)
-dt: Equi CA, CA_LOW, dt, default=0.002 (2 fs)
-maxwarn: Total number of warnings allowed for the equilibration, default=0
-nt: Total number of threads to start, default=0
-ntmpi: Number of thread-MPI threads to start, default=0
-gpu_id: List of GPU device id-s to use, default=””

Production

Simulation production

usage: production.py [-h] -f F -p P -o O -n NAME [-time TIME] [-dt DT]
                     [-maxwarn MAXWARN] [-nt NT] [-ntmpi NTMPI]
                     [-gpu_id GPUID]

Named Arguments

-f: Input PDB file
-p: Topologie in gromacs format .top
-o: Output Directory
-n: Output file name
-time: Production time, default=10
-dt: Equilibration dt, default=0.002 (2 fs)
-maxwarn: Total number of warnings allowed for the equilibration, default=0
-nt: Total number of threads to start, default=0
-ntmpi: Number of thread-MPI threads to start, default=0
-gpu_id: List of GPU device id-s to use, default=””

Peptide related:

Create peptide

Create a linear peptide structure, do a minimisation and a vacuum equilibration

usage: create_peptide.py [-h] -seq SEQ -o O [-m_steps MIN_STEPS] [-time TIME]

Named Arguments

-seq: Peptide sequence
-o: Output Directory
-m_steps: Minimisation nsteps, default=1000
-time: Vacuum equilibration time(ns), default = 1ns

Minimize cyclic peptide

Minimize a cyclic peptide structure in 2 steps, the first step without bonds constraints and the second step with bonds constraints

usage: minimize_pdb_and_cyclic.py [-h] -f F -n NAME [-dir OUT_DIR]
                                  [-m_steps MIN_STEPS] [-keep] [-cyclic]
                                  [-nt NT] [-ntmpi NTMPI] [-gpu_id GPUID]
                                  [-keep_segid] [-add_ter]

Named Arguments

-f: Input PDB file
-n: Output file name
-dir: Output directory for intermediate files
-m_steps: Minimisation nsteps, default=1000
-keep: Flag to keep temporary files (without flag output directory will be delete
-cyclic: Flag to indicate if the peptide/protein is cyclic
-nt: Total number of threads to start, default=0
-ntmpi: Number of thread-MPI threads to start, default=0
-gpu_id: List of GPU device id-s to use, default=””
-keep_segid: Flag to indicate if the original chain/segid should be kept
-add_ter: Flag to indicate if TER line should be included between chains and if residues in the input pdb file have non-consecutive residues

Insert n copy of a peptide in a system

Create a peptide strucure, insert it around a protein and do the minimisation, equilibration and production.

usage: sim_pep_prot.py [-h] -seq SEQ -npep NUM_MOL [-Pep_time PEP_TIME] -fsys
                       F_SYS -psys P_SYS -ssys S_SYS -o O -n NAME [-dt DT]
                       [-em_steps EM_STEPS] [-dt_HA DT_HA] [-HA_time HA_TIME]
                       [-CA_time CA_TIME] [-CA_LOW_time CA_LOW_TIME]
                       [-maxwarn MAXWARN] [-PROD_time PROD_TIME] [-nt NT]
                       [-ntmpi NTMPI] [-gpu_id GPUID]

Named Arguments

-seq: Peptide sequence
-npep: Number of molecule to insert
-Pep_time: Peptide vacuum equilibration with no constraint time(ns), default = 1ns
-fsys: Input PDB file of the system
-psys: Topologie in gromacs format .top of the system
-ssys: Input tpr file of the system
-o: Output Directory
-n: Output file name
-dt: Equilibration dt, default=0.005 (5 fs)
-em_steps: Minimisation steps, default = 5000
-dt_HA: Equilibration dt, default=0.005 (5 fs)
-HA_time: Equilibration with HA constraint time(ns), default = 0.25ns
-CA_time: Equilibration with HA constraint time(ns), default = 1ns
-CA_LOW_time: Equilibration with HA constraint time(ns), default = 5ns
-maxwarn: Total number of warnings allowed for the equilibration, default=0
-PROD_time: Production time(ns), default = 100ns
-nt: Total number of threads to start, default=0
-ntmpi: Number of thread-MPI threads to start, default=0
-gpu_id: List of GPU device id-s to use, default=””

~/Documents/repository/gromacs_py/equi_3_step.py -f 1y0m_water_ions/em/em_1y0m_compact.pdb -p 1y0m_water_ions/top/1y0m_water_ions_water_ion.top -o 1y0m_water_ions/ equi/ -n 1y0m -HA_time 0.1 -CA_time 0.2 -CA_LOW_time 0.4

Script

Tutorial

Topologie related:

Create topologie

Named Arguments

Solvate a system

Named Arguments

Simulation:

Energy minimization

Named Arguments

Equilibration

Named Arguments

Production

Named Arguments

Peptide related:

Create peptide

Named Arguments

Minimize cyclic peptide

Named Arguments

Insert n copy of a peptide in a system

Named Arguments