To be sure. I also tried Dr. Axel tutorial on topotools. I ran the input file for the nve ensemble and checked the output.
input script for topotools tutorial step 2a
units real
boundary p p p
atom_style full
read_data data.step2a
interaction styles
pair_style lj/cut/coul/cut 12.0
bond_style harmonic
angle_style harmonic
#dihedral_style opls
pair_modify mix geometric tail yes
OPLS considers 1-4 interactions with 50%.
special_bonds lj/coul 0.0 0.0 0.5
force field parameters
pair_coeff 1 1 0.066 3.5 # CT
pair_coeff 2 2 0.03 2.5 # HC
the remaining parameters are inferred from mixing.
bond_coeff 1 340.0 1.09 # CT-HC
angle_coeff 1 33.0 107.8 # HC-CT-HC
initialize random velocities and run a few steps
of MD to break symmetries.
velocity all create 100.0 53244 dist gaussian mom no rot no
fix 1 all nve
run 100
The output
Step Temp E_pair E_mol TotEng Press
0 100 100.26402 136.55858 331.91043 25047.343
100 123.16058 71.967028 110.05967 299.13744 -14673.19
The energy is not conserved. Please correct me if my interpretation is wrong ??
Thanks
Arun
To be sure. I also tried Dr. Axel tutorial on topotools. I ran the input file for the nve ensemble and checked the output.
input script for topotools tutorial step 2a
units real
boundary p p p
atom_style full
read_data data.step2a
interaction styles
pair_style lj/cut/coul/cut 12.0
bond_style harmonic
angle_style harmonic
#dihedral_style opls
pair_modify mix geometric tail yes
OPLS considers 1-4 interactions with 50%.
special_bonds lj/coul 0.0 0.0 0.5
force field parameters
pair_coeff 1 1 0.066 3.5 # CT
pair_coeff 2 2 0.03 2.5 # HC
the remaining parameters are inferred from mixing.
bond_coeff 1 340.0 1.09 # CT-HC
angle_coeff 1 33.0 107.8 # HC-CT-HC
initialize random velocities and run a few steps
of MD to break symmetries.
velocity all create 100.0 53244 dist gaussian mom no rot no
fix 1 all nve
run 100
The output
Step Temp E_pair E_mol TotEng Press
0 100 100.26402 136.55858 331.91043 25047.343
100 123.16058 71.967028 110.05967 299.13744 -14673.19
The energy is not conserved. Please correct me if my interpretation is wrong ??
What interpretation of what? Ever heard of a thing called equilibration?
Please get yourself some proper training in MD basics. A mailing list is not the right place for that.