Water and Salt Solutions

water_box.pdb was created from charmm water.inp, we will use this pdb file to perform amber simuation.

cp water_box.pdb to ./Pure/

vi, replace "TIP3" to "WAT", "OH2" to "O"

:%s/TIP3/WAT /g

:%s/OH2/O  /g


source leaprc.ff14SB
source leaprc.tip3p
loadAmberParams frcmod.ions1lsm_1264_tip3p

loadAmberParams frcmod.ions34lsm_1264_tip3p

loadAmberParams frcmod.ionslrcm_cm_tip3p
# Load the PDBs
water = loadPDB water_box.pdb

#Add ions

addIonsRand water xxx yyy

addIonsRand water CL 0

set water box {64 64 64}
# Save topology files
saveAmberParm water water_box.prmtop water_box.inpcrd
# Quit

xxx:type of ions


yyy:number of ions

tleap -f tleap.in


Minimization of water box 
   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 and equilibrating                                                              
   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,
&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:

Explicit solvent production run                                                        
   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,

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