I am trying to run an equilibrium MD simulation for an organic matter under NPT simulation (force field has been published in the literature). What I did at the beginning is to use
fix 1 npt temp 300.0 300.0 100.0 iso 100.0 100.0 100.0 (real units)
and use default control file from the examples (attached in the end).
What I have got from the output trajectory file is that the ensemble keyword shows as “NVE” and timestep length is 250 fs. I searched some posts on the mailing list and it seems that the control file is still developing.
So I am not sure if I have to specify “ensemble” keyword in control file or I should just focus on input script? Meanwhile, is there a possible way to dump different types of atom force values (e.g. non-bonded, Coulumbic, bond, angle) into a file during the simulation?
Thanks in advance.
attached is control file
simulation_name RDX_example ! output files will carry this name + their specific ext
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
nbrhood_cutoff 5.0 ! near neighbors cutoff for bond calculations in A ## Previous test was 4.5
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
thb_cutoff 0.001 ! cutoff value for three body interactions
write_freq 10000 ! write trajectory after so many steps
traj_title RDX ! (no white spaces)
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file