Dear Carlos,
First of all, what a nice project!
I want to simulate plasmids (dsDNA with circular topology).
However, the bonds connecting start-to-end do not seem to be connected during the simulation.
All steps followed from the example starting from PDB (and removing the protein part) work fine.
Even the simulation seems to run with constant energy and temperature.
Only after visual inspection of the trajectory I noticed the circular DNA object breaks.
I think it has to do how the pdb file deals with standard residue bonds only.
But I haven't found a way to by-pass or introduce this exception of circular topology.
Do you have any suggestions to make the code work with circular topology as well?
Of course I am happy to help!
Starting pdb and coarse grained pdb (generated with openMM) containing a plasmid of 500 bp
coarse_grained_plasmid_500.txt
atomistic_plasmid_500.txt
Dear Carlos,
First of all, what a nice project!
I want to simulate plasmids (dsDNA with circular topology).
However, the bonds connecting start-to-end do not seem to be connected during the simulation.
All steps followed from the example starting from PDB (and removing the protein part) work fine.
Even the simulation seems to run with constant energy and temperature.
Only after visual inspection of the trajectory I noticed the circular DNA object breaks.
I think it has to do how the pdb file deals with standard residue bonds only.
But I haven't found a way to by-pass or introduce this exception of circular topology.
Do you have any suggestions to make the code work with circular topology as well?
Of course I am happy to help!
Starting pdb and coarse grained pdb (generated with openMM) containing a plasmid of 500 bp
coarse_grained_plasmid_500.txt
atomistic_plasmid_500.txt