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lorenzo-rovigatti / oxDNA

A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings
https://dna.physics.ox.ac.uk/
GNU General Public License v3.0
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Compute energy without running the simulation #107

Open swapnilbaral-git opened 3 weeks ago

swapnilbaral-git commented 3 weeks ago

Is your feature request related to a problem? Please describe. I ran a LAMMPS/CGDNA simulation (oxDNA2) and considered comparing the energies computed by the simulation for a selected structure with the energies computed by standalone oxDNA2. I want to see that all energies computed by these two methods agree.

Describe alternatives you've considered I have energies computed by LAMMPS/CGDNA. To obtain energy computed by oxDNA2, I ran energy minimization and used the energies corresponding to 0th step to make the comparison with LAMMPS/CGDNA computed energies. I see that kinetic energy agree but the potential energies do not. So I have two questions:

1) Is there a way to spit out the energies corresponding to a given confirmation/structure without running a simulation just by using a) oxview, or b) any script ? 2) My understanding is that there should be no conversion factor between oxDNA potential energy and LAMMPS potential energy. Please let me know if I am in correct. I want to mention that I am aware that oxDNA energies are computed per particle.

lorenzo-rovigatti commented 3 weeks ago

Hi!

  1. I don't know of any third-party tools that can be used to compute the energy.
  2. I'm not familiar with the LAMMPS implementation, but I would be surprised if they used different units of measurement.

Just out of curiosity by how much do they differ?