1.系統的准備：
假設有一個PDB文件含有500多個殘基並且構成兩條鏈。首先修飾PDB文件：除去remarks, connectivity data 和 HETATM lines的數據(不包括晶體水)，然后增加TER標簽在蛋白鏈間和改變一些氨基酸的名字如：HIS to HIE, HID or HIP；和CYS。
tleap -s -f leaprc.ff99SB (告訴tleap將載入ff99SB力場，接下來載入蛋白）
> mol = loadpdb protein.pdb (這將增加氫到結構中)
> solvatebox mol TIP3PBOX 12.0 （加12埃的水盒子）
> charge mol （檢查分子的電荷）
> addions mol Na+ 0 （增加抗衡離子來中性化系統）
> saveamberparm mol protein.prmtop protein.inpcrd （創建prmtop and inpcrd文件）
> quit
protein.prmtop文件含有分子拓撲性，力場參數，原子和殘基名字。rotein.inpcrd文件含有起始的坐標文件，用這兩個文件產生PDB文件。
ambpdb -p protein.prmtop < protein.inpcrd > protein_solvated.pdb
2.能量最小化:
將運行兩步最小化：第一步固定蛋白最小化水分子位置，第二步最小化整個系統。當運行sander時，應該用控制文件：min1.in 和 min2.in
energy minimization stage 1
&cntrl
imin=1, maxcyc=5000, ncyc=2500,
cut=10.0, ntb=1,
ntc=1, ntf=1,
ntpr=10,
ntr=1,
restraintmask=':1-500',
restraint_wt=2.0
/
Information in the input file:
imin=1 perform minimization
maxcyc=5000 maximum number of minimization cycles
ncyc=2500 method of minimization will be switched from steepest descent to conjugate gradient after ncyc cycles
cut=10.0 specify the nonbonded cutoff, in Angstroms
ntb=1 periodic boundary, constant volume
ntc=1 SHAKE is not performed (for better energy convergence)
ntf=1 force evaluation, complete interaction is calculated
ntpr=10 every ntpr steps energy information will be printed in human-readable form to mdout file
ntr=1 flag for restraining specified atoms using harmonic potential
restraintmask=':1-500' string that specifies the restrained residues
restraint_wt=2.0 the weight (in kcal/mol-A^2) for the positional restraints
運行：sander -O -i min1.in -p protein.prmtop -c protein.inpcrd -o protein_min1.out -r protein_min1.rst -ref protein.inpcrd
mdin control data for the min/md run ；prmtop molecular topology, force field, atom and residue names ；inpcrd initial coordinates
mdout user readable state info and diagnostics ；rstrt final coordinates and velocities ；refc reference coords for position restraints
energy minimization stage 2
&cntrl
imin=1, maxcyc=10000, ncyc=5000,
cut=10.0, ntb=1,
ntc=1, ntf=1,
ntpr=10,
/
運行：sander -O -i min2.in -p protein.prmtop -c protein_min1.rst -o protein_min2.out -r protein_min2.rst
3.加熱
給系統加熱從0K到300K並在體積不變下帶有位置限制運行50ps動力學。
heating
&cntrl
imin=0,irest=0,ntx=1,
nstlim=25000,dt=0.002,
ntc=2,ntf=2,
cut=10.0, ntb=1,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
tempi=0.0, temp0=300.0,
ntr=1, restraintmask=':1-500',
restraint_wt=1.0,
nmropt=1
/
&wt TYPE='TEMP0', istep1=0, istep2=25000,
value1=0.1, value2=300.0, /
&wt TYPE='END' /
imin=0 do molecular dynamics ；irest=0 flag to restart the run, no effect ；ntx=1 no initial velocity information ；nstlim=25000 number of MD-steps to be performed
dt=0.002 time step (psec) ；ntc=2 flag for SHAKE, bonds involving hydrogen are constrained ；ntf=2 force evaluation, bond interactions involving H-atoms omitted
ntwx=500 every ntwx steps the coordinates will be written to mdcrd file ；ntt=3 use Langevin thermostat ；gamma_ln=2.0 collision frequency in temperature regulation
tempi=0.0 initial temperature ；temp0=300.0 reference temperature ；nmropt=1 varying conditions ；TYPE='TEMP0' varies the target temperature
istep1=0, istep2=25000 change is applied over steps istep1 through istep2 ；value1=0.1, value2=300.0 values of the change corresponding to istep1 and istep2, respectively
運行：sander -O -i heat.in -p protein.prmtop -c protein_min2.rst -o protein_heat.out -r protein_heat.rst -x protein_heat.mdcrd -ref protein_min2.rst
4.平衡
為了平衡系統，將運行500ps的分子動力學在常壓下沒有位置的限制
equilibration
&cntrl
imin=0, irest=1, ntx=5,
nstlim=250000, dt=0.002,
ntc=2, ntf=2,
cut=10.0, ntb=2, ntp=1, taup=2.0,
ntpr=500, ntwx=500, ntwr=5000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
/
Information in the input file:
irest=1, ntx=5 restart calculation, requires velocities in coordinate input file ；ntb=2 periodic boundary, constant pressure ；ntp=1 flag for constant pressure dynamics, md with isotropic position scaling
taup=2.0 pressure relaxation time (in ps) ；ntwr=5000 every ntwr steps during dynamics, the restrt file will be written, ensuring that recovery from a crash will not be so painful
運行：sander -O -i equil.in -p protein.prmtop -c protein_heat.rst -o protein_equil.out -r protein_equil.rst -x protein_equil.mdcrd
5.Production dynamics
在常壓下運行10ns動力學。獲得的軌跡被用於分析
production dynamics
&cntrl
imin=0, irest=1, ntx=5,
nstlim=5000000, dt=0.002,
ntc=2, ntf=2,
cut=10.0, ntb=2, ntp=1, taup=2.0,
ntpr=1000, ntwx=1000, ntwr=50000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
/
prod.in文件於equil.in的差異主要在於nstlim, ntpr, ntwx, and ntwr值的不同
當運行five million MD-steps時，他是合理的平行的運行：
mpirun -np 32 sander.MPI -O -i prod.in -p protein.prmtop -c protein_equil.rst -o protein_prod.out -r protein_prod.rst -x protein_prod.mdcrd