computing bond distance

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1

Dear Users;

I need to compute bond length for a boron nitride nanotube. my script is as follows:

2

Dear Users;

I need to compute bond length for a boron nitride nanotube. my script is as follows:

this won’t work, since the tersoff potential you are using does not have explicit bonds (like in an amber, charmm, gromos, OPLS/AA or similar force field), but computes them implicitly and thus can handle bonds breaking and changing bond order.

now if your system does not exhibit and bond breaking or formation during the MD run, you can do one of the following two things:

  1. write a software/script that does the bond length analysis directly from the trajectory file. (just need to do a nested loop going over all pairs of atoms, determine the closest pair according to periodic boundaries and add to the histogram, if the distance is within a typical range of B-N bonds, which can be found out from computing the g® / RDF. where the bond cutoff would be the distance of the minimum after the first peak).

  2. a) run the simulation without compute bond/local.
    b) create a new data file for atom style bond (not atomic), in which you provide a bond connectivity (note, that you will have to include bonds going across periodic boundaries!)
    c) write a new input where you use lj/cut for pair potential (just assign some arbitrary values like epsilon 0.0 and sigma 3.5 with cutoff 5.0) and also define a bond style (e.g. harmonic with force constant 0 and equilibrium distance of 1.446) and this time you can include compute bond/local since you now define explicit bonds
    d) instead of “run” use the “rerun” command perusing the trajectory file from the previous simulation with the tersoff pair style. the fact, that you have no interaction energy doesn’t make a difference, because, the trajectory was created with the correct forces and energies, and you are only using this to do the bond length analysis.

axel.

1 Like
3

Thank you for your answer

you mentioned in part (2-b) that I should " create a new data file for atom style bond (not atomic) " . but I don’t know how to do that. I used to create data file by VMD, but I thinks it don’t create data file for atom style bond. So I would be thankful if you let me know how to do that.

Regards;
Reza

4

Thank you for your answer

you mentioned in part (2-b) that I should " create a new data file for atom style bond (not atomic) " . but I don’t know how to do that. I used to create data file by VMD, but I thinks it don’t create data file for atom style bond.

you are thinking incorrectly. the TopoTools plugin in VMD can write data files in atom style bond.

So I would be thankful if you let me know how to do that.

please look it up in the TopoTools documentation. that is what the documentation is for.

axel.