Running Molecular Dynamics



# Read the full peptide structure (after linking and building);
echo off;
read peptide.min.ammp;
echo on;

# Update full non-bonded list when atomic displacement;
# greater than 0.75 angstroms;

setf mxdq 0.75;

# Set the temperature to 300 Kelvin;
setf temp 300;

# Use bond, angle, hybrid, torsion, non-bonded terms for forcefield;
use none bond angle hybrid torsion nonbon;

# Initialize atomic velocities with a boltzmann distribution;
v_maxwell temp;

# Check the energies prior to MD run;
monitor;

# Do 5 ps of molecular dynamics;
# Every 1 ps check energies and output a structure;

seti i 0;
loopi end: i 5;
tpac 1000 .00001 temp; # 1000 steps of 1 fs;
echo on;
monitor; ;
echo off;
output peptide.md.ammp i;
dump atom bond angle hybrid torsion nonbon velocity; close;
end: ; # label designating end of loop;
exit;