[lammps-users] Output configuration after NVE integration

Dear LAMMPS users,

I am trying to estimate the time for unwinding of DNA beads from the cylindrical protein. For the initial configuration I generated the input data
using python(dataconfiguration28.LAMMPS) and read the data in LAMMPS. After NVE integration I dumped all the coordinates and visualised the output but

could not see the unwinding of the DNA beads (red beads) from the cylinder (green). In order to fix this, I ran the simulation for five times as a trial but no changes.

When I checked the output data (outff30.xyz) after NVE integration, the input data(dataconfiguration28.LAMMPS) and the output are same and hence no changes in

the final configuration.

Though this is my research problem, if anyone can point out where I am doing the mistake, it will be of great help for me to fix the mistake. I am also trying
to find the mistake meanwhile.

I am using LAMMPS 29 October 20 version in Ubuntu 18.04 and have attached the input script.

unwrap.in (1.62 KB)

chromosome.eps (135 KB)

dataconfiguration28.LAMMPS (35 KB)

Your simulation is for 50000 timesteps at 0.005fs. that is a total simulation time of 250fs. Not much can happen in such a short time.

Thank you axel…I will run it for longer time period.

I don’t think that will make that much of a difference, since you are restricting the temperature to around 1K with a very short thermostat time constant. that will “freeze” your system. the timestep is also unusually small for particles of the mass that you have. There are other inconsistencies in your system, like that you define bond types and a bond style but have no bonds in the data file. these are all very unusual settings and look like you have copied bits and pieces from very different models with settings for very different purposes (and unit settings).

You also should figure out on what time scale anything should happen and whether that is attainable with the simulation settings you choose within the amount of time you can wait for the results.

thank you for the comments Axel and for pointing out the bond style information.
The pair style I have implemented is also not the accurate one except the Morse
interaction which is the main interaction between DNA and protein.

I will understand the system set up and revise the code completely again,
In the literature it has been reported that 10-50 ms the DNA will be in the unwrapped state,
and i will check that after fixing other issues.