运行分子动力学模拟

Create script file named runmd.sh

#!/bin/bash

# CREATE the mdin file

cat > mdin << EOF

equilibration for box

&cntrl

imin=0, ntpr=3000, ntwx=3000,

ntx=1, irest=0,

tempi=298., temp0=298., ntt=3,

gamma_ln=5., ntb=2, ntp=1, taup=1.0, ioutfm=1, nstlim=3000000,

ntwr=1000, dt=.001, ig=-1,

/

EOF

# Run sander command.

sander -O \

-i mdin \

-o md1.out \

-p ionicbox.prmtop \

-c min1.x \ # The restart file from minimization

-r md1.x \$RUN.rst7

-x md1.nc \

-e md1.dat

Once again, you should look at the Amber manual to understand what exactly this input file is doing.

Note: The restart file generated from MD simluations contains velocity information that the restart file from minimization did not have. To address this difference, use ntx=5 and irest=1 for future simulations to denote that the restart file (that is, the new input coordinates file) indeed contains the velocity information for sander to process.

Also note: when you run the next simulation, use the restart file from the previous output as your new input coordinates file.

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