Guide for Molecular dynamics (MD) simulations with AMBER Software on ASU Sol cluster

Initial steps with PDB

Follow the PyMOL guide here: PyMOLGuide

Using VPN to connect to ASU network:

Follow the VPN guide here: VPNGuide

Before you continue

• Change my id to yours in each command
• If you are using a pdb file other than 1btl.pdb, rename it to 1btl.pdb so you dont have to change anything else in the scripts

After logging in:

pwd command shows me home directory /home/ikazan

change directory to scratch space

cd /scratch/ikazan

create a new directory here by using

mkdir -pv testdir1

change directory to the new one

cd testdir1/

ls

the directory is empty

pwd shows me the current working directory

copy the sol path: /scratch/ikazan/testdir1

open a new ternminal tab (this will be connected to your own computer)

go to the directory where you have the pdb file and copy the file to sol

scp ./1btl.pdb ikazan@login.sol.rc.asu.edu:/scratch/ikazan/testdir1/

we are going to switch the termnial window to the sol session one

we are going to start an interactive session by running

interactive

Paremetrize Protein with LEaP

Prepare tleap.in input file:

vim tleap.in

press i to enter edit mode

copy and paste the text below

source leaprc.protein.ff14SB
source leaprc.water.tip3p
pdb_file = loadpdb 1btl.pdb
solvateBox pdb_file TIP3PBOX 16.0
charge pdb_file
addions pdb_file Na+ 0
addions pdb_file Cl- 0
saveAmberParm pdb_file 1btl.parm7 1btl.crd
quit

press esc button on keyboard and then type :wq

run:

module load amber/22v3

and then run:

tleap -f tleap.in

Minimize Solvent

Prepare minimization_solvent.in input file:

vim minimization_solvent.in

press i to enter edit mode

copy and paste the text below

# Energy minimization solvent
&cntrl
imin=1,
ntpr=10000,
ntr=1,
restraintmask='!(:WAT,Na+,Cl-)',
restraint_wt=10.0,
maxcyc=50000,
ncyc=25000,
ntc=1,
ntf=1,
ntb=1,
cut=12.0,
&end
/

press esc button on keyboard and then type :wq

Two options to continue: 1) Interactive, 2) Batch (I recommend 2)

1) Interactive mode

make sure you have interactive session and run:

module load amber/22v3

run:

pmemd -O \
-i minimization_solvent.in \
-o minimization_solvent.out \
-p 1btl.parm7 \
-c 1btl.crd \
-r 1btl_minimization_solvent.rst7 \
-x 1btl_minimization_solvent.crd \
-ref 1btl.crd

2) Batch mode

Prepare minimization_solvent_sbatch file:

vim minimization_solvent_sbatch

press i to enter edit mode

copy and paste the text below

#!/usr/bin/env bash
#SBATCH -n 8
#SBATCH -p general
#SBATCH -t 7-00:00:00
#SBATCH -o slurm.%j.out
#SBATCH -e slurm.%j.err

module load amber/22v3

mpiexec.hydra -n 8 pmemd.MPI -O \
-i minimization_solvent.in \
-o minimization_solvent.out \
-p 1btl.parm7 \
-c 1btl.crd \
-r 1btl_minimization_solvent.rst7 \
-x 1btl_minimization_solvent.crd \
-ref 1btl.crd

press esc button on keyboard and then type :wq

submit the job to queue by running

sbatch minimization_solvent_sbatch

to check the status of the job run

squeue -u ikazan

Minimize Solution

Prepare minimization_solution.in input file:

vim minimization_solution.in

press i to enter edit mode

copy and paste the text below

# Energy minimization solution
&cntrl
imin=1,
ntpr=10000,
maxcyc=100000,
ncyc=50000,
ntc=1,
ntf=1,
ntb=1,
cut=12.0,
&end
/

press esc button on keyboard and then type :wq

Two options to continue: 1) Interactive, 2) Batch (I recommend 2)

1) Interactive mode

make sure you have interactive session and run:

module load amber/22v3

run:

pmemd -O \
-i minimization_solution.in \
-o minimization_solution.out \
-p 1btl.parm7 \
-c 1btl_minimization_solvent.rst7 \
-r 1btl_minimization_solution.rst7 \
-x 1btl_minimization_solution.crd

2) Batch mode

Prepare minimization_solution_sbatch file:

vim minimization_solution_sbatch

press i to enter edit mode

copy and paste the text below

#!/usr/bin/env bash
#SBATCH -n 8
#SBATCH -p general
#SBATCH -t 7-00:00:00
#SBATCH -o slurm.%j.out
#SBATCH -e slurm.%j.err

module load amber/22v3

mpiexec.hydra -n 8 pmemd.MPI -O \
-i minimization_solution.in \
-o minimization_solution.out \
-p 1btl.parm7 \
-c 1btl_minimization_solvent.rst7 \
-r 1btl_minimization_solution.rst7 \
-x 1btl_minimization_solution.crd

press esc button on keyboard and then type :wq

submit the job to queue by running

sbatch minimization_solution_sbatch

to check the status of the job run

squeue -u ikazan

Heat up System

Prepare heatup.in input file:

vim heatup.in

press i to enter edit mode

copy and paste the text below

# Heat Up 100ps
&cntrl
imin=0,
ntx=1,
irest=0,
ntpr=5000,
ntwr=5000,
iwrap=1,
ntwx=5000,
ntr=1,
restraintmask='!(:WAT,Na+,Cl-)',
restraint_wt=10.0,
nstlim=50000,
dt=0.002,
ntt=3,
temp0=300.0,
tempi=0.0,
ig=-1,
tautp=1.0,
gamma_ln=2.0,
ntp=0,
taup=2.0,
ntc=2,
ntf=2,
ntb=1,
cut=12.0,
&end
/

press esc button on keyboard and then type :wq

Two options to continue: 1) Interactive, 2) Batch (I recommend 2)

1) Interactive mode

make sure you have interactive session and run:

module load amber/22v3

run:

pmemd -O \
-i heatup.in \
-o heatup.out \
-p 1btl.parm7 \
-c 1btl_minimization_solution.rst7 \
-r 1btl_heatup.rst7 \
-x 1btl_heatup.crd \
-ref 1btl_minimization_solution.rst7

2) Batch mode

Prepare heatup_sbatch file:

vim heatup_sbatch

press i to enter edit mode

copy and paste the text below

#!/usr/bin/env bash
#SBATCH -n 8
#SBATCH -p general
#SBATCH -t 7-00:00:00
#SBATCH -o slurm.%j.out
#SBATCH -e slurm.%j.err

module load amber/22v3

mpiexec.hydra -n 8 pmemd.MPI -O \
-i heatup.in \
-o heatup.out \
-p 1btl.parm7 \
-c 1btl_minimization_solution.rst7 \
-r 1btl_heatup.rst7 \
-x 1btl_heatup.crd \
-ref 1btl_minimization_solution.rst7

press esc button on keyboard and then type :wq

submit the job to queue by running

sbatch heatup_sbatch

to check the status of the job run

squeue -u ikazan

Production NPT (CPU)

Prepare production_npt_cpu.in input file:

vim production_npt_cpu.in

press i to enter edit mode

copy and paste the text below

# Production 100ps
&cntrl
imin=0,
ntx=5,
irest=1,
ntpr=5000,
ntwr=5000,
iwrap=1,
ntwx=5000,
nstlim=50000,
dt=0.002,
ntt=3,
temp0=300.0,
ig=-1,
tautp=1.0,
gamma_ln=2.0,
ntp=1,
taup=2.0,
ntc=2,
ntf=2,
ntb=2,
cut=12.0,
&end
/

press esc button on keyboard and then type :wq

Two options to continue: 1) Interactive, 2) Batch (I recommend 2)

1) Interactive mode

make sure you have interactive session and run:

module load amber/22v3

run:

pmemd -O \
-i production_npt_cpu.in \
-o production_npt_cpu.out \
-p 1btl.parm7 \
-c 1btl_heatup.rst7 \
-r 1btl_production_npt_cpu.rst7 \
-x 1btl_production_npt_cpu.crd

2) Batch mode

Prepare production_npt_cpu_sbatch file:

vim production_npt_cpu_sbatch

press i to enter edit mode

copy and paste the text below

#!/usr/bin/env bash
#SBATCH -n 8
#SBATCH -p general
#SBATCH -t 7-00:00:00
#SBATCH -o slurm.%j.out
#SBATCH -e slurm.%j.err

module load amber/22v3

mpiexec.hydra -n 8 pmemd.MPI -O \
-i production_npt_cpu.in \
-o production_npt_cpu.out \
-p 1btl.parm7 \
-c 1btl_heatup.rst7 \
-r 1btl_production_npt_cpu.rst7 \
-x 1btl_production_npt_cpu.crd

press esc button on keyboard and then type :wq

submit the job to queue by running

sbatch production_npt_cpu_sbatch

to check the status of the job run

squeue -u ikazan

Production NPT (GPU)

Prepare production_npt_gpu.in input file:

vim production_npt_gpu.in

press i to enter edit mode

copy and paste the text below

# Production 20ns
&cntrl
imin=0,
ntx=5,
irest=1,
ntpr=5000,
ntwr=5000,
iwrap=1,
ntwx=5000,
ntwv=-1,
ioutfm=1,
nstlim=10000000,
dt=0.002,
ntt=3,
temp0=300.0,
ig=-1,
tautp=1.0,
gamma_ln=2.0,
ntp=1,
taup=2.0,
ntc=2,
ntf=2,
ntb=2,
cut=12.0,
&end
/

press esc button on keyboard and then type :wq

Two options to continue: 1) Interactive, 2) Batch (I recommend 2)

1) Interactive mode

make sure you have GPU active session

interactive -G a100:1

run:

module load amber/22v3

run:

pmemd.cuda -O \
-i production_npt_gpu.in \
-o production_npt_gpu.out \
-p 1btl.parm7 \
-c 1btl_production_npt_cpu.rst7 \
-r 1btl_production_npt_gpu.rst7 \
-x 1btl_production_npt_gpu.nc

2) Batch mode

Prepare production_npt_gpu_sbatch file:

vim production_npt_gpu_sbatch

press i to enter edit mode

copy and paste the text below

#!/usr/bin/env bash
#SBATCH -N 1
#SBATCH -n 6
#SBATCH -G 1
#SBATCH -p general
#SBATCH -t 1-00:00:00
#SBATCH -o slurm.%j.out
#SBATCH -e slurm.%j.err

module load amber/22v3

pmemd.cuda -O \
-i production_npt_gpu.in \
-o production_npt_gpu.out \
-p 1btl.parm7 \
-c 1btl_production_npt_cpu.rst7 \
-r 1btl_production_npt_gpu.rst7 \
-x 1btl_production_npt_gpu.nc

press esc button on keyboard and then type :wq

submit the job to queue by running

sbatch production_npt_gpu_sbatch

to check the status of the job run

squeue -u ikazan

Analyze the MD simulation

Follow the MDEvaluationGuide guide here: MDEvaluationGuide