Compute energy without running the simulation

[swapnilbaral-git]

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]

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?

[ErikPoppleton]

I'm not sure if this is what you're looking for, but in oxDNA Analysis Tools there is output_bonds which given a configuration and an input file, uses the oxDNA energy model to compute the energy of each individual term in the interaction potential. For example if you run

oat output_bonds input configuration.dat

You will get an output which looks something like:

#id1 id2 FENE BEXC STCK NEXC HB CRSTCK CXSTCK DH total, t = 607000000
0 1 0.0414132 0.0 -1.11994 0.0 0.0 0.0 0.0 0.0 -1.07852
0 2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.000134116 0.000134116
1 2 0.0456133 0.0 -1.14283 0.0 0.0 0.0 0.0 0.0 -1.09722
1 3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.000369632 0.000369632
2 3 0.00818457 0.0 -1.22545 0.0 0.0 0.0 0.0 0.0 -1.21726
2 4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.000244062 0.000244062
3 4 0.00311354 0.0 -1.34097 0.0 0.0 0.0 0.0 0.0 -1.33786
3 5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00030874 0.00030874
4 5 0.0064446 0.0 -1.33258 0.0 0.0 0.0 0.0 0.0 -1.32613
4 6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.000630652 0.000630652
5 6 0.161738 0.0 -1.20651 0.0 0.0 0.0 0.0 0.0 -1.04477
5 7 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.000588574 0.000588574
...

The first two columns give the IDs of two particles which interact, and the subsequent columns give the value of each term from the potential used in the input file.