copy md_npt.pdb to ./WATERBOX_AMBER/PURE
in vim, replace "TIP3" to "WAT", "OH2" to "O"
:%s/TIP3/WAT /g
:%s/OH2/O /g
tleap.in
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source leaprc.ff14SB source leaprc.tip3p loadAmberParams frcmod.ions1lsm_1264_tip3p #Load the PDBs water = loadPDB md_npt.pdb # Set box dimention set water box {64 64 64} # Save topology files saveAmberParm water water_box.prmtop water_box.inpcrd # Quit quit |
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source leaprc.ff14SB loadAmberParams frcmod.ions34lsm_1264_tip3p
loadAmberParams frcmod.ionslrcm_cm_tip3p #Add ions addIonsRand water xxx yyy addIonsRand water CL 0
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xxx:type of ions
NA MG AL CL
yyy:number of ions
tleap -f tleap.in
Minimization:
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Minimization of water box &cntrl imin = 1, ! Turn on minimization ncyc=1000, ! If ncyc<maxcyc steepest descent before switching to conjugated gradient for remaining maxcyc = 5000, ! Total number of minimization cycles cut = 8, ! Nonbonded cutoff in angstroms ntpr=100, ! Print frequency / |
pmemd.cuda -O -i min.mdin -o min.out -c water_box.inpcrd -p water_box.prmtop -r min.rst
Heating:
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heating and equilibrating &cntrl imin=0, irest=0, ntx=1,ntxo=2, ntpr=100, ntwx=100, nstlim=20000, dt=0.002, ntt=3, tempi=50.0, temp0=300, gamma_ln=5.0, ig=-1, ntc=2, ntf=2, cut=8, iwrap=1, ioutfm=1,ntrelax=100, / &wt type='TEMP0', istep=50.0,istep2=5000,value1=0.0,value2=300.0 / &wt type='TEMP0', istep=5001,istep2=20000,value1=300.0,value2=300.0 / &wt type='END' / |
pmemd.cuda -O -i heat.mdin -o heat.out -c min.rst -p water_box.prmtop -r heat.rst
Production Run:
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Explicit solvent production run &cntrl imin=0, irest=1, ntx=5,ntxo=2, ntpr=100, ntwx=100, nstlim=1000000, dt=0.002, ntt=3,ntp=1, temp0=300, gamma_ln=5.0, ig=-1, ntc=2, ntf=2, cut=8, iwrap=1, ioutfm=1,ntrelax=100, / |
mpirun -np 2 pmemd.cuda.MPI -O -i md.mdin -o md.out -c heat.rst -p water_box.prmtop -r md.rst -x md.mdcrd